Here's some of the theories for each
Cyndaquil: I don't think Ash would be very keen on having another Fire Type evolve that soon after the Charizard incident. Heck, if he couldn't control his Quilava, the thing might very well set is pants on fire repeatedly. While this would've been a wonderful gag, such misfortunes are reserved to happen to Team Rocket, not Ash
Totodile: Totodile was too busy dancing around and chasing love interests that he didn't have time to be focused on evolution.
Squirtle: Squirtle was iconic as a Squirtle. It just wouldn't be the same if he were to become Wartortle or Blastoise.