I would agree that MSH vs SF probably is the best game in the VS. series, but there are some aspects of it I didn't like.
First off, it was the only game in the series that didn't feature any new characters (Norimaro aside; he wasn't even in the US version). Capcom just rehashed fighters from the Zero series and X-men/MSH. As such, MSH vs. SF has the worst line-up of characters of any of the VS. games. The main Marvel characters were fine (Spiderman, Capt. America, Hulk, Wolverine) but the supporting cast they chose were throw-offs from the earlier games. Characters like Shuma Gorath, Blackheart, Cyclops, and Omega Red shouldn't have been in the game - they're not really representative of the main Marvel universe (Cyclops and Omega are pure X-men characters, Blackheart and Shuma Gorath are obscure characters from lesser known series). Capcom should have included more respectable Marvel characters like Dr. Doom, Thor, Punisher, or Dr. Octopus. And adding Dan and Sakura to a SF list already consisting of Ryu, Ken, and Gouki makes for too many shotos on the SF side.
I would have liked original backgrounds as well. Again, this is the only game in the series that reused backgrounds. It makes it seem less like a true sequel and more like an update.
I sort of missed the X vs. SF end battle where you went against your partner too. It was kind of interesting to fight one on one after you spent so much time depending on tagging your teammate. Plus sometimes you could get burned for choosing a strong partner to compensate for that weaker character whose ending you wanted to see.
But all and all the good outways the bad. MSH vs. SF is the only game whose striker system I liked. Plus it was the first game in the series where Capcom started to alter it's characters significantly (ie. changing Ken's fireball and hurricane kick, changes to Sakura). The hidden characters were pretty cool as well, particularly Mega-Zangief. Fighting Mech Gouki was much better than going against Apocalypse, Onslaught, or Abyss. And I liked the endings for MSH vs. SF; particularly Dan's and Gouki's.
So while there were some disappointing aspects of MSH vs. SF that could have readily been avoided, all and all it probably is the pinacle of the VS series.