Was Survival Hunter spec the superior one in ulduar or was it MM??
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I believe that the general consensus is that Survival was considered to be stronger than MM prior to ToC release and subsequent gearing. MM really only gets strong when you can achieve a high base (passive from gear, excluding Gems, enchants, etc.) ArP of somewhere thereabouts 700-800, depending on your source. Because of this, MM really suffers prior to the saturation of ArP gear that ToC and ICC brought to the table.
Realistically, if you could achieve a high ArP rating with really specific, weird gearing, you might see some different numbers than expected. Most of the theorycrafting that's been done for Wrath assumes 3.3.5a+ICC gearing/BIS, so I don't believe much has been done to really hammer out the hard science of Naxx and Ulduar numbers, though I could be wrong and I just haven't stumbled upon the data yet.
ToC numbers are somewhat exempt from this, as many people use ToC gear for ICC gearing, a lot of work has been done to flesh out what the best "Pre-ICC" or "ICC entry" gear/spec combo is.
Realistically though, if you have vastly more experience with MM than Surv., I would just recommend you ignore the science and stick with MM. You're going to have a pretty decent numbers drop as you relearn everything, and reteach yourself relevant muscle-memory. Prior to soft ArP cap, all of the specs for hunter benchmark somewhat closely, so taking that into consideration a smooth "inferior" spec play will almost always pull better real-world numbers than a sloppy "superior" spec.
Again, just my two sense, and it's not really backed up by that much hard data (other than theorycrafting for ICC level content). Take it as you will, but hope that I helped.
Also see <http://forum.warmane.com/showthread.php?t=415962> as from my reading, it contains some relevant information, and some more brief opinions apart from my own.
(P.S: Feel free to PM me in game @Yenih if you want to collaborate or theorycraft things in real time. I always think things like this are beneficial, especially with how little hard-data is out there, in-game experience sharing means quite a bit at this stage in the game.)
Edited: April 23, 2020