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I would pick Cyndaquil since he's cool and may not look much at his basic stage But when he evolves into his final form oh boy the Rampage has begun
Other things i liked about Cyndaquil are as followed
-Being able to learn Thunder punch at his Third evolution
-Great Attack Special attack and Speed
-The ability to carry you through the whole game with just him as your Pokemon (I've done it myself)
I always pick Cyndaquil, haha. Chikorita wasn't useful (but cute!) and Totodile was nah, I didn't like its moves and wanted other water pokémon in the game.
Cyndaquil has always been my pick in the GSC era; when it fully evolved to Typhlosion, it was really fast and pretty strong with it's fire-type moves! Though sometimes I change it up to Totodile so I don't have to worry about finding a pokemon that could use Surf. Growlithe would serve as a Fire type then.
First choice would be Cyndaquil now that Ive gone with it plenty of times then Totodile. Ive only ever used Chikorita 2-3 times but it might be because of having to deal with the first gym that I picked it less.
I almost always use(d) Totodile. While it wasn't as good before the split, it was still the most capable overall for me. Being able to learn Ice Punch was a huge deal because of how strong Dragons were back in this gen. Chikorita was always fun to use as a challenge but was and still is underwhelming. Cyndaquil is adorable, but always made the early parts way too easy being able to mow down sprout tower and Bugsy :(
Cyndaquil. I was originally a water starter girl (Squirtle, Totodile) - but at some point before Gen III was released I replayed my cartridges with fire starters and have never gone back. I almost always go with a fire starter. The only exception to this was when I got Sun. Litten/Incineroar just looked pathetic....
I'll give Chikorita some love if no one else does!
I've chosen Chikorita in probably 75% of my GSC/HGSS playthroughs. I like grass types and the Chikorita line in particular just really appeals to me aesthetically. I generally choose appearance over usefulness. I just want to use my favs and I'll deal with the downsides they might bring along.
I have used the other two though. I like Cyndaquil too, the Totodile line not too much.
When I first played GSC, my initial choice was Totodile as it was my favourite at the time. Now though, I'd probably say I prefer Cyndaquil and perhaps even Chikorita over Totodile.