Our buddy Ghostcrawler has appeared on the forums answering (or re-answering, as he says) a few concerns about the balance of the game. Most of his answer is about PvP: he says that Death Knights and Holy Pallies are overpowered, but that while Blizzard does believe there are more imbalances, debate is still raging about exactly where they are. And he does say that while burst damage is still a concern, he feels that Blizzard did a lot to combat that when they started Season 5, and that the bigger concern now is getting mana pools under control. Too many fights now have healers just going and going, and while they don't want fights to end super fast, they can't all drag out, either.
He also talks more in-depth about the balance between gear you can get from PvP and PvE and how it needs to be fixed: he straight out says that 25-man Naxx is too easy to PuG, and agrees that Ulduar and future PvP weapons "should ideally require the same amount of investment." Likewise, when Blizzard tried to reset the resilience stacking at the start of Season 5, they had players facing very powerful weapons from the PvE raids like Kel'thuzad, which lead to, as he says, "a perfect storm for fast Arena deaths." Which is probably why so many players left the Arenas.
The plan for the future? Ulduar's hard modes will be way tougher than Heroic Naxx, so players won't be able to PuG PvE and then go kill in PvP right away. Of course Death Knights are still cruising for a nerfing, if patch 3.1 doesn't bring them down off their high Deathcharger. And GC suggests that in the future, starter PvP gear may beef up resilience at the cost of offensive stats, so that players don't begin with gear that has great defense and offense right away.