A couple years ago when I did a marathon of all Pokémon main series, I picked each starter in every Gen II game. Here, I have only two versions, so I had to make a choice... and it was easy: not Chikorita, never Chikorita (sorry ^^').
So, Cyndaquil in Gold, Totodile in Silver. Exactly the opposite of what I did when I got Silver, then Gold versions on GBC when I was a kid.