Well mega is more of just a buff if you ask me. Do some more damage and take some more hits, and look awesome.

As for abilities, yeah have fun within the known boundaries. For example, I'm going to be using my Lucarios more like Lucario from Smash Brothers xD like the OP says, League Rules are out of the way so the Pokemon don't have to use moves like a JRPG. Want your Pokemon to go into a relentless rampage at the sound of your trainer screaming in fear? Go for it. 

Giving your Pokemon excessive power is okay temporarily, if you find the right time and reason for it. In other words, make a good story out of it. That's what we're here for! That being said... My Pokkemon Team isn't very shiny beyond the Pokemon names, but I think I may have overdone my history.