bubble does not autocancel at all.
Dthrow sounds bugged, you can cc between hits of dsmash normally and hit squirtle
Bubble is a special so it cannot auto-cancel, it could Land Cancel like falco's blaster but thank god it does not.
CC is only good if you have a good CC option and lots of characters (falcon, dorf) don't
I'm starting to think that waterfall is straight up broken
Dair is fine. Squirtle doesn't really have cc problems imo. His real problems are his lack of range, lack of moves positive on shield, terrible tech roll, and bad players (me included). All of his aerials are great and have their own uses, dair included. You may just need to work on answering cc, TKD
Lack of range is part of his design, you make up for his lack of range with his extreme mobility. And on many moves like bubble, watergun, bair, d-smash, uair, up-B, he has quite a bit of range.
Lack of moves positive on shield? Most characters don't have those, I think you mean safe on shield, and squirtle does have those, Bair and Nair can be safe on shield when landed at the bottom of the shield. D-tilt is -6 and puts you below a lot of grabs (and D-tilt comes out Frame 3!) I would say it's safe on shield a LOT.
Squirtle's tech roll is bad for a reason, if you don't tech and go into knockdown then hold away many times squirtle can slide rapidly across the stage to the ledge and escape. He is also very difficult to hit or grab (if your movement is up to snuff) so tech chasing is supposed to balance how difficult it is to break neutral on him.