I think that Capcom planned to invest several efforts on the 3DS and made efforts to develop the platform. For one thing, note the way Monster Hunter 4 and Resident Evil Revelations were prefaced by stepping stone games. Monster Hunter 3G and 4 were both unveiled at a Nintendo event, if I recall, and Revelations was featured heavily in earlier 3DS promotions.
Let's say Capcom had made a deal to lock Monster Hunter onto Vita. Well, they don't have a deal to stop making Vita games entirely: they've already made at least one. So if they were interested in investing in the platform, one would think they would have already done so with other games.
We've seen several Capcom games released for the 3DS that started development before launch. If Capcom started development on multiple Vita games before launch, where are they? Where are the signs that they existed? In fact, wasn't the big shock at Sony's TGS show after the MH4 announcement that Capcom was only talking about games they were porting to the system?
There's no way that deals weren't made. But I think that Capcom saw themselves as the big fish in the small PSP pond. They wanted a big userbase, and it was mutually beneficial for to Capcom and Nintendo to catalyze that.
Similarly, look at the enhanced port of Resident Evil Revelations. If we assume Capcom always like to port everything everywhere, it seems strange that there's no Vita version announced. They're making a PS3 version, aren't PS3-Vita ports supposed to be extremely easy? DuckTales and Chronicles of Mystara are similar, I think.
Other cases that may be related are Sengoku Basara 2 Heroes and Monster Hunter G. The both were ported - probably on the cheap - to the Wii. They both served as precursors to the next major entry in their series, both of which had the Wii as their lead platform.
Well, you probably know this already, but 3rd didn't sell double 2nd G either.
And I know Sammy Samusu is in here to correct me, but the MH fanbase in general seems to love the G expansions. 2nd G > 2nd, 3G > 3. But anyway, I digress.
To support Sammy's point. The new monsters in 2ndG versus 3G (excluding subspecies, which are modified versions of existing monsters):
2ndG: Brachydios, Dire Miralis
3G: Nargacuga, Queen Vespoid, King Shakalaka, Hypnocatrice, Lavasioth, Ukanlos
2nd G also added Felyne (one of MH's major mascot) companions. 3G does not have them, and it also lacks Tigrex (a highly popular monster that was already in Portable 3rd). 3G was also outsourced to Eighting and had fairly low projections (1.2 million or so), which implies that it was not considered to be a major title.