The best replacement for totodile is squirtle.

The best alternatives to totodile are rated as following:
★★★★★  squirtle
★★★  cyndaquil crystal
★★★  cyndaquil heartgold
★★★  piplup
★★★  cyndaquil
★★★  chikorita
★★  kingdra
★★  sneasel
★★  totodile
★★  mudkip
★  wooper
★  gyarados
★  cyndaquil silver
★  oshawott
★  sandile
★  gible
  cyndaquil better
  monferno and cyndaquil
  chikorita silver

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totodile
squirtle
cyndaquil crystal