Capcom can't re-release X-Men vs. Street Fighter because Activision still holds the rights to the X-Men games titles. The reason we won't be getting Marvel Super Heroes vs. Street Fighter is because it's the weakest installment in the Marvel Vs. library.
It's been confirmed by Capcom's representative "Sven" that X-Men vs. Street Fighter nor Marvel Super Heroes vs. Street Fighter won't be included in Marvel vs. Capcom Origins for the following reasons.
The first is pretty obvious, but it's been confirmed that X-Men vs. Street Fighter won't be included because the name "X-Men" appears in the game's title and Activision holds the rights to the name brand of X-Men titles. The reason Marvel Super Heroes vs. Street Fighter won't be included is because Capcom feels it's the weakest and most lacking of the Marvel Vs. series, which is actually true.
As a member of the fighting game community I'm fine with the two titles we'll be receiving in Marvel vs. Capcom Origins. Marvel Super Heroes is really where Capcom made the foundation of the whole Marvel Vs. series (building upon Children of the Atom of course) and Marvel vs. Capcom is basically a improved version of Marvel Super Heroes vs. Street Fighter. All in all, I'd say we got the better games, but that's just my opinion.
Here's the trailer of Marvel vs. Capcom Origins if you haven't seen it yet.