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Cyndaquil definately! Tis my favourite. Chikorita is quite bland and totodile just isn't my style.
For Gen I & II i picked the fire type as these are harder to find in the wild. By gen III I decided I would just pick the ones I liked rather that going for a set of pokemon that would have no type disadvantages overall.
Gen I & FR/LG : Charmander
Gen II & HG/SS: Cyndiquill
Gen III: Treecko
Gen IV: Turtwig
When I was younger I would have picked Chikorita, but now it's Totodile without a doubt, although I'm not really a fan of its evolutions. My favorite one of them fully-evolved is Meganium.
Totodile, as it's the starter I used in Gold (and Crystal). Cyndaquil is a close second, though. Chikorita's okay, but I don't like it as much as i like the other two.
Most say Cyndaquil's the best choice, and I like it alot. If it matters, I guess I could just point out my four starter favs: (the number means the generation)
Charmander
Cyndaquil
Mudkip
Turtwig
Wow, that was easier than I thought. I have no idea why I wrote all of them though.
Cyndaquill , well, but thats because in every pokemon game i start with the fire starter, offtopic- started fire in D/P/P too and that was my biggest pokemon disappointment ever :(
Come on! When I saw this forum I hoped you would include color games, because squirtle is my all time favorite starter! (Blastoise actually) Although if you are only doing II Generation, then it would be Cyndaquill.
To tell the truth, the earliest PKMN Game I've ever played is Ruby...
So I've never had to choose from the 2nd Gen starters! (Shocking, 'eh?)
But I will be choosing soon... (HG/SS)
Being a loyal fire fan, I'd have to go with Cyndaquil. I've never gone wrong with fire, and I always mono with it. :D Not to mention Typhlosion is complete and utter decimation contained in a red and white ball.