You know regular Gyrados is actually arguable better, though the Mega Form is amazing. For some reason You can't get stab Crunch so that made me sad ;/ As a Physical Train of Destruction he's pretty good but not as defensive because it makes him weak to Fairy, Fighting, and Bug. If your opponent predicts this it can suck... Regular Gyrados is better defensively for it's typing as long as you avoid Rock and Electrics, and if you invest in training Sp. Def for EV's he can take up to THREE Thunderbolts (when combo'd with HP EV's). Not too shabby if I say so myself...
Yeah my best advice is to just run through the game, everything's easier to do at the end. You also want to get the Hatching O-Power - and worship it. It's a little tricky to obtain.
I could give you a couple EV trained 4/5 mons to kick the games ass with, therefor allowing you to breed stuff sooner :P if you so Desire. Got some leftover Gale Wing Fletchlings... Bulbasaurs... Phantumps... <.< I got what you need to make E4's life hell.