It's been a long time since I felt the need to agonize over what spec I want to play on my hunter in raids. Usually there's one clear cut winner, but in Siege of Orgrimmar both survival and beast mastery are doing pretty darn well. Maybe we're not putting out warlock numbers, but we're well into the upper half of the charts when it comes to DPS. The recent hotfix to Aspect of the Hawk gave us just enough of a kick to keep us competitive as everyone continues to gear up. Marksmanship has cemented itself as a popular PvP spec in 5.4, and maybe it's OK that one spec is more PvP oriented. At least we have large numbers of hunters playing all three specs -- it's not a luxury we've always had in the past.
One of the most common questions I see from new hunters is what spec should they play for the best DPS? It's difficult to answer such a question, and it reminds me a lot of the "what is the best pet?" question. If we're talking about PvE it really comes down to beast mastery vs. survival. I haven't forgotten about marksmanship, but in my opinion it's just not as versatile for raiding this tier, or this entire expansion for that matter. As for choosing between survival and beast mastery, the best place to start is to learn the differences.