I went with Totodile in Gold. I always start with the water type started in my main file for a generation, though since gen 2 was only the second gen, I'm not sure if that pattern was fully established yet. I liked the look of Totodile the best, and I loved my water type Squirtle, so Totodile seemed like a good pick. I didn't like the way its evolved forms looked, though, so I never evolved it.
I started with Cyndaquil when I started Silver a year or two later, and chose Totodile again in Crystal. I've never been a big fan of the Chikorita line.