Definitely Totodile line! I never really got to like Squirtle for anything other than its design, as I've barely even used it, since both of the other starters of its generation overshined it in pretty much every aspect. Charmander was really popular amongst pretty much everyone at the time that the first generation games were big, and Bulbasaur was just easy to get through the games with, whereas Squirtle never really benefitted the progress in any way that the other two didn't, so I never really felt a reason to use it. After I learned that Grass types were also good against Rock types, I instantly switched over to Bulbasaur.
Totodile, however, was probably the strongest of the three starters in the second generation. How I felt about Squirtle quite generally fell upon Chikorita in this generation, except, unlike Squirtle, the game was significantly harder to get through in the beginning if you chose Chikorita, which of course provided a much bigger challenge, but was also quite annoying, so I either went with Cyndaquil or Totodile. And yeah, though Cyndaquil might've been my first choice most of the times, in a battle of being the favourite between the Squirtle line and the Totodile line, it's definitely the winner.