With the exception of some large targets (Wario, if he counts as a large target), I find myself having the easiest time picking off big hitters (Ike notwithstanding). Charizard is only a threat to Pit if you let it become a threat. One simple strategy I use, and I'm sure this is not new, is to pluck Arrows after Arrows after Arrows and force Charizard to approach me. Its side-stepping and roll dodging isn't that great, so you still have a bit of an advantage. Its BAir is like a slower version of Pit's, so approaching an airborn Charizard with its back to you is risky, unless you space you attack (very easy with Pit's glide attack and FAir). If you take Charizard on face-to-face, watch out for Rock Smash; that hurts like hell.
Ivysaur has some powerful aerials as well as its USmash. Spacing won't work well here because if the opponent knows what they're doing, they too will be spacing, and Ivysaur's attacks already have great range to begin with. Being a tether-recovery dependant, I like to gimp Ivysaur every chance I get. Repeated BAir (or FAir since that's easier) to hit them further away from the stage (or completely out of the stage's boundry, resulting in a KO, but anyway), then make sure Ivysaur cannot grab the ledge afterwards. And don't worry about Ivysaur gimping you during a WoI recovery...Ivysaur doesn't have many options there.
Squirtle...hmmm...fast attacks, nice combos, a hard to stop BForward, nice aerials, and its a small target. For Pit, Squirtle may be the more difficult of the Trainer's three Pokémon. You can't really rush this battle, unless Squirtle makes a dumb move, and camping isn't effective, what with Squirtle's BFoward, small size, and speed; more so than any of the other Pokémon, Squirtle can approach you with no promblems.