I'm choosing Cyndaquil. He was my very first starter (my first game was Pokemon Silver) and I'm quite fond of 3 of the 4 Fire starters. I know Cyndaquil breaks the early game, and it makes life easier, but I still like Cyndaquil. Besides, I prefer Elite Four challenge where I am extremely underleveled.
On my second run-through, I'll probably choose Chikorita. I'd pick Chikorita more often if I liked Meganium's design better. I love Bayleef's design, but Meganium's...
And I'm not into Totodile, so... Cyndaquil or Chikorita.