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The main problem is that Totodile is so blatantly better than the other two starters when it comes to beating the game that it wasn't even funny
Ingame wise, Chikorita is by far and wide the absolute worst starter of all time sporting a tank/cleric moveset and having huge disadvantages against almost all gyms and the Elite 4
Cyndaquil isn't -bad- but back then the fire type wasn't all that useful, all he could do was fire attack + thunder punch, and he was pretty frail
Totodile had good stats on pretty much all areas, water was by far the most useful type between the three, you could give it Ice Punch as soon as you got to Goldenrod (in the remakes he'd just learn Ice Fang my level up by then), he could make good use of Dig or Earthquake, Bite and Crunch wre handy against psychics or ghosts, and besides Lt. Surge and Eirika he'd have super effective moves against most gyms/E4 and be either neutral or resist against them as well.
