I'm not going to address any balance issues, be it BM pets or atrocious Disc regen, but I'd like to mention some things that are far more irritating, and yet uncontroversial.
1. It seems that in MoP once you join an Arena game, you're in a new raid. This means raidmarks are removed, and the order of Compact raid frames is based on entrance order.
Previously raidmarks would stay if you queued as a marked raid.
Also the "player" unit was always at the bottom of the raid frame stack.
Having to put new marks every time is very irritating (even with macros, because the leader changes), and having the player raid frame in a random place may even cost you games - and is something you can't fix without code taint.
2. Another issue is that if someone uses macros that have a couple /cast lines (covers all 3 options from a tier for example), and then relearns inside arena, the macro will stop working (You'll get a message that you didn't learn the spell).
3. Sometimes when you respec you lose action bar abilities that are not in spellbook anymore, which means you need to make macros just to keep a single spell, so that it's never removed.
4. Now that a lot of classes have a vanish-like abilities on a short cooldown, it has become increasingly irritating to be forced to reapply focus to get the frame back. Maybe it would be good to change the mechanics so that it's still there, you just can't act on it for the duration of vanish/invis.
I realise those are UI issues, but they directly influence competitive PvP and I wish Blizzard would spend some time reviewing this. I'm sure I've missed a few other issues, but if only the first one was looked at, I'd already be content.