On my playthrough of Omega Ruby, literally half my team were Megas. But I really like 5 out of all the ORAS Megas*. Sorry for this essay here, too. Read it if you want to, skip it if you don't. ^ . ^;
5. Mega Metagross - The Metagross that I used on my team was the shiny distribution event, so I was excited to play the game with it, and it really made me happy when Steven and other characters actually addressed the Metagross if you had it on your team. However, the thing, I love it and I hate it at the same time. On one hand, it is an incredibly powerful Pokemon, with a base stat total of 700. On the other hand, it was already such an over - powered Pokemon, I'm not so sure it merited having a Mega. The only reason I actually enjoyed Mega Metagross is because of the final battle with Steven - had it not been able to go Mega, the battle itself would have been relatively easy. I enjoyed the challenge; I didn't even care for using it in my team as much as I did battling Steven's! I was especially happy upon defeating the Elite Four and Steven with just Bonnie, my (lvl 100) Lopunny. Even with 6IVs, the Mega Stone, and the maxed out level, the final battle was still pretty damn difficult.
4. Mega Pidgeot - I fell in love with Pidgeot's design when I saw it. I was also happy to hear that Pidgeot, a pretty sub-par Pokemon in terms of competitive builds, got a Mega. Its boost in Special Attack came as a bit of a surprise, but I rolled with the punches when I did my research to build my 5IV Pidgeot, Icarus. No Guard, grouped with that 135 SpA and the move Hurricane makes this Pokemon a beast. Not to mention, it can learn Heat Wave, which is a pretty powerful, multi hitting move that can potentially OHKO two of its weaknesses - Ice and Steel. All in all, I was very happy with this guy.
3. Mega Altaria - One of my major disappointments with X/Y is that it introduced the Fairy type, went on and on and on about how Fairies are so powerful against Dragons and all, and then made the psuedo-legendary (Goodra), A, a Pokemon that was not a Fairy type, and that, B, was a freaking Dragon type. With the overall "feminine" design, Goodra would have made an amazing Dragon/Fairy dual typing! But, nope, let's just throw another Dragon pseudo legendary in the mix, because we totally need more of those. Point is, this is why I was so excited to hear about Altaria's Mega. I played through the story with an Altaria, Alia, on my team, and it kicked a lot of butt as a Mega.
2. Mega Sceptile - This guy was a Pokemon that, in my opinion, was pretty "meh" before ORAS. If you want me to be honest here, I fell in love with Mega Sceptile for very similar reasons that I fell in love with Mega Altaria. The main difference between the two, and the reason Sceptile is set before Altaria, is because while Mega Altaria was a cool bonus for a Pokemon that I already loved, Mega Sceptile made me fall in love with a Pokemon that I was pretty impartial to. Had it not been for the fact that Mega Sceptile got the typing it did (which I wish Serperior had), I likely wouldn't have given it a second glance when choosing my starter.
1. Mega Lopunny - I may just be a bit biased here, but I'll go ahead and say what I'm going to say: my Buneary (Bonnie, the same one mentioned earlier), was a gift to me from one of my friends and was the first 6IV Pokemon I have ever owned. In addition to that, Lopunny was one of my constants through Gen 4. But all that said, there's not really much I can't love about Mega Lopunny - its design is wonderful, it gets appropriate boosts that turns it into a Pokemon fit for my battling method, its move pool pretty much nullifies all of its weaknesses, and its ability allows it, as a Normal/Fighting type, to hit Ghost types, and hard.
*Please realize that I'm only giving my opinions on my favorites from the ones that I have actually used. Also, my opinions are not shaped by the Pokemon themselves but by the situations in which they were used.