Thor was actually pretty bad in Vanilla MVC3 but got all buffs in UMVC3. Still no one really cared for him. The players who played him used him on terribly optimized Thor teams (Abegen and RoyalFlush). Plus Thor is notorious for getting rushed down by Wolverine and Vergil type characters so the meta game used to not favor.
Now the meta game has shifted to super jump flight characters who can zone (Morrigan, Zero, Magneto). This favors Thor greatly as he fights almost exclusively in the air, he is weak on the ground. He still has to worry about Dark Vergil but so does every other character so that is not unique weakness for him. His damage was already high but his other main weakness was that he got nothing from his air throw which meant that Thor players need to make hard reads with his command throw.
In addition, the advent of plink dashing has made Thor much better mobility wise. Thor with Bolts is insanely good, those 2 characters go really well together. Also Thor's Mighty Smash assist is a legit CC assist that can shutdown Dark Vergil and other in your face characters.
IMO Thor is considerably better than Haggar in the meta game. I have always maintained this. I still don't think Thor players are at that level but this guy is the closest to unlocking Thor's potential.