You may have four copies of a card with the same in your deck, except energies (you may have as many as you want) and Ultra Prism (new card your only allowed to have one copy of). You may have more than one mega, but I don't suggest it.
I've played cards for years and use a team that disables (via sleep/paralyze/confusion) such Pokemon and take them out quickly. This would give me massive advantage because I'd draw 2 prize cards.
Edit: An even better point (since I decided to correct a few things on this old post of mine) is that you want your evolution lines to be a nice 1:1:1/1:1 ratio, meaning that if your only using this mega once, the other mega and basic EX get wasted; you could have had 2 more cards in your deck that actually do get used.
So, yes, you can, but it will usually not work out. (Not to mention most EX's either can't use the same attack twice, have recoil, or lose energies. But that may be "fixed" with other cards) Mega's aren't bad, I use some, it is just hard to manage more than one.
Hope I helped!