Oh hey the thread is alive.
Venusaur being part Flying type gives me an amusing image. Anyways, Flying/Fairy does have quite a lot of weaknesses unfortunately, so 
Filter can work well with regular Venusaur. That, or 
Regenerator to help with its weakness to SR. Ground/Fairy is good coverage, which is why I'd suggest 
Adaptability for Mega Venu, giving it immediate power after Mega-Evolving.
Any one of the Charizard formes should probably have 
Levitate, to cover the Ground weakness. Going with the roles I suggested above (regular Char as set-up sweeper, M-Char X as bulky attacker and M-Char Y as hit-and-runner), I'd give it to M-Char X, allowing it to take the EdgeQuake coverage relatively well. Regular Charizard can have 
Multiscale to help it with setting up, I suppose, and it wouldn't even be too powerful when compared to the mega formes, as they both get the 100 stat boosts. For M-Char Y, I have no idea. Either 
Flash Fire for more chances to switch in and the boosted fire moves, or 
Download to get the potential boost in power.
On Blastoise, I agree with 
Phione's suggestion of 
Magic Bounce and 
Scrappy, but I think Magic Bounce should go to Mega Blastoise to give it an edge over regular Blastoise, as the mega losts its item slot. 
Cursed Body would've been good if it doesn't only have a 30% chance of activating, as it can then force many spinblockers to switch out. I don't think we're supposed to change how abilities work in this pet mod, right?