Hunter DPS and scaling
Hunter dps was where we wanted it to be in Naxx. Two problems arose in the Ulduar tier. First, we improved the dps of other pure classes, especially rogues. We have a small change coming up that should slightly improve hunter dps to make up for this and will apply to all level 80 hunters. (But do not assume you are going to see a 20% dps jump when we make this change.)

The second problem is that in order for hunter dps to improve, they must upgrade their bow and arrows. A rogue by contrast needs two weapons and a Ret paladin one weapon. However, a higher tier of arrows was not available anywhere. Because dropping arrows as loot feels cruddy, we handled this in the past through a rep grind. We can't just give the arrows away to fresh level 80s or hunter dps will be too high relative to other classes. Long term, we have a different solution for arrows, but that won't help in Ulduar. So the change we made was to let bows (and guns) scale more than other weapons to make up for the "missing" ammo. The ammo is baked in to the weapon damage.

We didn't think this was a problem for the 10-player case because the melee and casters are not getting weapons with such large stat increases. The Ulduar 10 loot is slightly better than the Naxx 25 loot, but only slightly (it depends a lot on how many 226 items you were able to get). Since we said Naxx 25 wasn't a problem (in our eyes), Ulduar 10 isn't a problem either. (If you think your Naxx damage was too low I can understand how you might feel differently, but that is not our position.)

Players have a tendency to sometimes invoke "scaling problems" as a generic explanation for why they need buffs. However, in this case it was truly 100% a scaling problem. Scaling problems only happen when characters acquire better and better gear -- literally as gear stats increase, some classes might not be benefiting as much as others so balance at one tier goes away at higher tiers. The weapons in Ulduar 25 with their relatively large stat increases had this problem. The weapons in Ulduar 10 with their slight or null stat increases did not (though they will in the next tier of content, as will the Ulduar 10 hard mode weapons)