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The first time I played through it, I used Cyndaquil. The only reason I picked it is so that I could get through the game easier and quicker. It's sort of cute, I guess. I've taken quite a liking to it. However, my real favorite is Chikorita, which is what I picked the second time through. Meganium is just pure awesome.
cyndaquil on crytal and first time on hg
second totadile
3rd and 4th chikorita, but i just culdnt use him. you dont need a grass type in johto. stuck him in the day care
I went for Cyndaquil in SoulSilver. As for HeartGold, Totodile. Mainly because Feraligatr has access to an ever-useful Ice moves (Ice Punch notably), and Waterfall is pretty good.