Totodile is available as the Water-type starter Pokémon in the Johto-based games.
Totodile is one of the most reliable and useful starter Pokémon since the Dawn Stone of time. With a great Atk stat, a usable Sp Atk stat, just enough speed, and decent bulk, Totodile stands at the top of the list of many great Water-types in a region that is highly favorable toward them. Totodile has an amazing movepool by GSC standards in Rage, Headbutt, Strength, Surf, Ice Punch, and Earthquake which allows it to go head to head with all of the most threatening Pokémon in the game, such as Bugsy's Scyther, Whitney's Miltank, Chuck's Poliwrath, Clair's Kingdra, Lance's Dragonites... the list goes on. Additionally, Totodile can be a team player and use necessary moves like Whirlpool and Waterfall to progress in the game. There really is no downside with using Totodile and plenty of upside.
Rival (Cherrygrove City): Scratch, Scratch, and more Scratch. Or Rage, if you already have it.
Gym #1 - Falkner (Violet City, Flying-type): Literally all you have to do is spam Rage and you win. Rage is a very, very effective move. Equipping a Berry is recommended but not required.
Gym #2 - Bugsy (Azalea Town, Bug-type): Spam Rage and win. It is better to have a Croconaw here, though, because Scyther's Fury Cutter works in a similar way but runs off STAB, and a base 105 Attack, which is frightening for Totodile, and not too good for Croconaw either.
Rival (Azalea Town): It is actually possible to win this fight with a slightly overleveled Croconaw and the Fury Cutter TM, but it is not recommended as you will no doubt have at least one teammate who can take on Bayleef just fine. Its Razor Leaf and annexed high probability of critting is seriously scary for Croconaw.
Gym #3 - Whitney (Goldenrod City, Normal-type): This is a very tough fight for any starter, but you win the majority of the time if you just spam Rage. It should be noted that, for whatever reason, the AI will not use Attract while you are using Rage. Still, Miltank's Speed and Stomp may prematurely end the Rage buildup, so prepare a backup in case you need it.
Rival (Burned Tower): Croconaw can will this fight singlehandedly by using Ice Punch, but again, it is not recommended to fight Bayleef or Magnemite, the new addition. Neither of them is good for Croconaw's health, should it not be OHKOed. However, if Croconaw has Dig, Magnemite is easy pickings.
Gym #4 - Morty (Ecruteak City, Ghost-type): You will have Surf by this point, so use that to your advantage (STAB neutral Surf outdamage a supereffective unSTAB'd Bite). You will probably have to switch out at least once due to Curse and/or Hypnosis, however. For this reason, it is highly recommended you equip a Mint Berry which can be found on the route just west of Ecruteak, right beside the Moo Moo Farm.
Eusine (Cianwood City, Crystal only): Headbutt flinch/Strength the Drowzee to death and Surf the Haunter. His Electrode does, however, carry THUNDER, so definitely avoid that matchup even if you already have a Feraligatr.
Gym #5 - Chuck (Cianwood City, Fighting-type): Poliwrath is extremely bulky and resists your STAB, but Feraligatr can still probably win this fight barring extreme DynamicPunch hax; again, equipping a Mint Berry is definitely the way to go if you have one. Having Return greatly helps here.
Gym #6 - Jasmine (Olivine City, Steel-type): Feraligatr can use Dig against the Magnemite to beat them. Steelix is easily dismantled by Surf.
Rocket Executive battle #1 (Team Rocket HQ): This should be a clean sweep. There are explosive Pokémon here, but only the Electrode are likely to be anywhere near dangerous, as everything else is underleveled by Feraligatr standards.
Rocket Executive battle #2 (Team Rocket HQ): Another clean sweep. Gloom may not be as smooth, but the only Grass STAB it has is... Absorb. Just beat it.
Gym #7 - Pryce (Mahogany Town, Ice-type): It will take a while, but you can eventually get past the highly bulky Dewgong just by spamming Surf. Even better if you have Strength or Return. The other two 'mons are not an issue at all.
Rocket Executive battle #3 (Goldenrod Radio Tower): Just be mildly wary of Weezing exploding, but Feraligatr's good bulk should enable it to withstand that hit if need be. The Koffing are not an issue.
Rival (Goldenrod Underground): This will be a moderately tough fight, but it's nothing the gator can't handle. The Meganium is super bulky though, and has STAB Razor Leaf, so team support is recommended.
Rocket Executive battle #4 (Goldenrod Radio Tower): Same battle as the HQ, but with a Vileplume instead of a Gloom... which still only has Absorb as its Grass STAB of choice. Ice Punch it and Surf the rest.
Rocket Executive battle #5 (Goldenrod Radio Tower): Another big winner for Surf. Koffing can't even explode, so this is basically the easiest fight of the bunch.
Suicune (Bell Tower, Crystal only): The most damage Suicune can deal to Feraligatr is through Gust, or Rain Dance-boosted BubbleBeam. It shouldn't be a problem to defeat Suicune, whether with Dig, Strength, or Return.
Gym #8 - Clair (Blackthorn City, Dragon-type): You can muscle past all the Dratini/Dragonairs with Ice Punch. Kingdra will be a lot tougher to take down, but thankfully you resist its primary STAB attack, and DragonBreath won't be doing a whole lot. Just be ready to tank a Hyper Beam at all times; Feraligatr can do it at full health, but watch your HP bar.
Rival (Victory Road): This fight shouldn't be that big of a deal, especially since you can now easily OHKO his Haunter with Earthquake. Again, team support is recommended for Meganium.
Elite Four Will (Indigo Plateau, Psychic-type): Just use the right coverage move, be wary of stray Psychics, and win. Bite gets a honorable mention for Slowbro, which can be pretty difficult to take down otherwise, as it is very physically bulky.
Elite Four Koga (Indigo Plateau, Poison-type): Plenty of potential hax during this fight, but you should be able to 2HKO each 'mon at worst. The Forretress does have Explosion, but the AI is unlikely to select it on the very first turn, meaning you definitely will be able to knock it out first with Surf.
Elite Four Bruno (Indigo Plateau, Fighting-type): Just spam Surf or Earthquake and win. The Machamp will probably be able to 2HKO you with Cross Chop, but you should be able to PP stall it barring a crit (unlikely, due to Cross Chop having only 80% accuracy).
Elite Four Karen (Indigo Plateau, Dark-type): The Umbreon is probably one of the bulkiest 'mons you will ever face in any Johto run, so just try to outstall it if possible. Avoid the Vileplume as it can wipe you out with Petal Dance. The Gengar does have the lethal Destiny Bond, but just like with Explosion Forretress, it is not terribly likely to use it right away. However, this is a bigger risk than Forretress exploding, as there is no such thing as tanking a Destiny Bond. Consider your moves carefully.
Champion Lance (Indigo Plateau, Flying-type): Pretty much everything can and will use Hyper Beam, but because the alligator is a beast, it will always live one at full health unless you are super underleveled or get critted in the face. Definitely watch out for Thunder from the level 47 Dragonite, though; unless you are certain to outspeed, avoid that one.
From this point onwards, you can fight the gyms in any order, though you will need to retrieve the Machine Parts from the Cerulean City gym before you have access to the earlier portion of Kanto. Feel free to anticipate or postpone any battles as needed.
Gym #9 - Brock (Pewter City, Rock-type): Spam Surf and use Earthquake for Omastar and Kabutops, simple as that. Kabutops has Giga Drain, but off its low Special Attack it shouldn't be a problem.
Rival (Mt. Moon, optional): Aside from the ever-avoided Meganium, the other threat added to the present team is Alakazam. While Feraligatr's special bulk is good, Alakazam's special offensive is frightening, and you should use a special wall to take it on if you have one. Spam Earthquake and Surf against everything else.
Gym #10 - Misty (Cerulean City, Water-type): Earthquake or Return will work well here. Nothing much can hurt Feraligatr.
Gym #11 - Lt. Surge (Vermilion City, Electric-type): Despite the type disadvantage, Feraligatr should be at a high enough level to not really take a lot of damage from Electric moves. Earthquake should also off everything before Surge's Pokémon can land a hit.
Gym #12 - Erika (Celadon City, Grass-type): Ice Punch is a winner here. However, if possible, use something else against Victreebel and Bellossom, the main threats of her team. Victreebel should die to Ice Punch, but can hit back really hard if it doesn't, while Bellossom is specially bulky, probably enough to tank a hit.
Gym #13 - Janine (Fuchsia City, Poison-type): Everything is low levelled enough that Feraligatr can completely annihilate it. Use Earthquake, and Return or Surf for Crobat.
Gym #14 - Sabrina (Saffron City, Psychic-type): Special attackers aren't Feraligatr's thing. Unless very overlevelled, it is not advised to have Feraligatr fight anything but Mr. Mime. If you need to, you can probably take on Espeon or Alakazam, but Feraligatr is unlikely to have enough steam power for both of them.
Gym #16 - Blue (Viridian City): Ice Punch disposes of Pidgeot and Exeggutor. The latter only has SolarBeam for STAB, so it won't catch Feraligatr by surprise, even in the event it survives a hit. Surf does Rhydon and Arcanine in. Gyarados can be outmuscled with Return, but keep watch on your HP as it has Hyper Beam. For Alakazam, find a better alternative if possible, or use the same reasoning as Gyarados.
Rival (Indigo Plateau, optional): Again, don't let Feraligatr fight Meganium and have it avoid Alakazam too, if possible. The rest is much like usual.
Red (Mt. Silver): Pretty tough fight in general. The gator can actually survive a Thunder from Pikachu even if it is several levels lower, because Pika is NOT holding a Light Ball, and easily OHKO with Earthquake. Feraligatr takes on Charizard and Blastoise very well as long as you allow yourself to use healing items whenever necessary. Venusaur, Espeon and Snorlax will definitely pose a threat, but all of them can be hard checked by a Steel-type such as Skarmory or Scizor, and out of the three, Snorlax is the one that Feraligatr can outmuscle more easily, as it can tank physical hits well and Snorlax doesn't really like Return or Earthquake in its face. Still, healing will likely be needed.
Totodile unequivocally has by far the best movepool in all of GSC. Right off the bat, it has just Scratch and Leer, but it gets the incredibly useful Rage at level 7, which will enable it to singlehandly beat the first three gyms with a rather high success rate. Its first STAB is Water Gun at level 13. After that, at level 21 as Croconaw, Bite provides a decent coverage option as well. There's Scary Face at level 28 but it isn't really useful, and Slash at level 38 as Feraligatr, but both Strength and Return are available sooner and have higher base power. Screech at level 47 is useless, but you may consider Hydro Pump at level 58 over Surf, if you feel the need for more power in the late game.
As far as TMs go, the two most important options available for the gator are Ice Punch and Dig, which later meets an upgrade in Earthquake, both of which allow the gator to overpower its "counters". Also, Totodile's most powerful physical attack is Return, but this is only true if Totodile has reached maximum happiness. If that weren't sweet enough, the croc gets access to Surf just before the fourth gym, which is remarkably early. The gator is a team player as well, having various support options in Headbutt, Rock Smash, Cut, Whirlpool, and Waterfall, the use of the latter three being necessary to progress in the game.
Minimum stats are calculated with 0 EVs, IVs of 0, and a hindering nature, if applicable.
Maximum stats are calculated with 252 EVs, IVs of 31, and a helpful nature, if applicable.
Totodile Line Ratings
At what point in the game should I be evolved? Ideally, you should have a Croconaw by the time you reach the Bugsy fight, although it is entirely possible for Totodile to beat that matchup too. You definitely want to have a Feraligatr by the time you fight the fifth gym (Chuck), as otherwise his Poliwrath will probably overwhelm you.
How good is the Totodile line in a Nuzlocke? Without a doubt, Totodile is one of the two top-tier Pokémon in GSC along with Geodude. If, after reading this analysis, you're thinking that GSC Totodile is one of the most useful/reliable Pokémon in existence, then you'd probably be right. Totodile basically has zero bad matchups all throughout Johto, and the Pokémon which have a "type advantage" against the gator get throttled by the appropriate coverage move. If you are new to Nuzlocking and want to enjoy a very easy (and enjoyable!) playthrough, then the Gator is your best bet.
Weaknesses: Electric, Grass
Resistances: Water, Fire, Steel, Ice
Neutralities: Normal, Fighting, Flying, Poison, Ground, Rock, Bug, Ghost, Psychic, Dragon, Dark