Having been both Prot as well as holy, i have the benefit of being able to see pally tanks form both angles. Truth be told i do believe that the choice of using a pally or warrior tank should be based on the rest of the group's composition more than anything. Warrior tanks rely heavily on CC, and focusing on 1-2 targets at a time. It's easier to heal through, much less stressful, but also slower, and CC isn't always possible. Pally tanks excel in that the more mobs they take on, the better they get at holding aggro. CC is possible with pally tanks, but the less mobs a pally takes on at a time, the more mana inefficient he becomes. And let's not forget about redoubt.
Mana starts becoming a problem for really long fights with pallies, not so much with seal of wisdom, but the warrior rage mechanic means endless threat generation. No matter what's said about spiritual focus, as a tank i never found it to be completely adequate. You WILL run out of mana, and it WILL become a problem.
I think pallies also have a bit more trouble getting uncrittable/uncrushable, but that's down to gearing problems and that's out of our control at the moment. As for whether you'll get picked less if you're a pally, i never found that to be a problem. Some parties prefer pally tanks, but there isn't anything a warrior can do that a pally can't. There is alot that pallies can do that warriors can't though. Demo shout and such can't compare to consecrate for pure aggro generation.
Plus, prot warriors do have a hard time levelling, from what my warrior friends tell me. Most lvl and tank in arms up until their 60s i believe. might be wrong about that though. Prot pallies are fantastic at grinding wuest mobs and such. Mount up, aggro everything and just wait for all of it to die.