IMO, at a high level of play, Ganon is either even or has a slight advantage on both Ivysaur and Charizard, and he has a hard -2 against Squirtle. I'm sure a lot of you won't believe me, but I figure I'd give my opinion since I probably have more good PT exp than many of you have good Ganon exp.
Ivysaur is a bit harder than Charizard for Ganon because it's more difficult for Ganon to get inside. But it's still easier than a lot of you seem to think. Ganon's dash attack OoS is extremely dangerous for Ivysaur, because a lot of the time his dash attack completely beats out Razor Leaf, and if Ivysaur gets knocked into the air against Ganon, he's going to have a very hard time landing without taking at least one more hit. Ganon is much more dangerous to land against than most people realize.
If Ganon lands a side B against ANY of the three pokemon, he has a GUARANTEED ftilt (misses Squirtle but sends Ivysaur and Charizard offstage at a low angle that will result in a likely reverse Uair gimp at most %s), guaranteed Dtilt (sets up a juggle) and guaranteed dash attack (kills squirtle at less than 90% fresh, ivysaur at 100% fresh, and charizard at 110-115%ish fresh).
Ganon can have a hard time against Ivysaur's Bair, but as someone said, it's low risk, low reward. Except the problem is, the reward is too low considering how high Ganon's reward is if he manages to get inside. Honestly, in my smash career, likely over 80% of my kills on Ivysaur have been gimps. It's retardedly easy for Ganon to gimp Ivysaur. It does get a bit safer for Ivysaur if he knows how to cover his recovery with Razor Leaf, but it's still very easy for Ganon to gimp with reverse Uair, or in some cases dropoff Nair.
This is the easiest pokemon for Ganon to deal with IMO. He has a huge, clumsy hurtbox, gimpable recovery, bad landing options, and a moveset that really doesn't present Ganon with a lot of problems.
The most common strength I've heard you guys say that Charizard has over Ganon is flamethrower. And you're right, it is a pain for Ganon. It does make Charizard's landing safer, but not by THAT MUCH. If Charizard has to land on a platform, flamethrower isn't going to help him. And if he's landing on flat ground, in my experience Ganon can read the flamethrower and punish it if he knows what to do.
I'd go more into the matchup but I'm about to leave work. Suffice to say that in my experience, Ganon's moveset contends very well with Charizard's movesets in all aspects.
Squirtle is very tough for Ganon and most things you say about him are true. Squirtle can Utilt Ganon to over 50%, and outprioritzes a lot of Ganon's moves in the air. It sucks. Just don't side B against Ganon because he has a guaranteed warlock punch on you if he footstools you.
Let me know if you have any questions, I'll answer them when I get home.