Sure it does. MvC2 used sprites in a time where sprites were common for fighters. MvC2 didn't really sell enough copies to make up for the development cost (when it was released 10 years ago and even then it had 3D backgrounds). Street Fighter II HDR was delayed multiple times and Udon had to settle with less than stellar sprites because they ran out of time due to them taking so long to create (as well as having to outsource some of the work). BlazBlue CS (does BB CS use 3D backgrounds? Too lazy to launch it to check) is making up developing costs by including $60 worth of purchasable DLC on day 1 (at least it did for the Japanese version). Does Arcana Heart 3 even use HD sprites? At the end of the day, 3D is cheaper and faster to create content with, which means more development money to spend on actual gameplay stuff.
Oh and does the MT Framework even have the functionality for actual 2D games? If making a 2D sprite game requires making a new engine then yeah, no point in doing that. Also take into consideration the number of games Capcom develops simultaneously compared to Examu and Aksys Games and then probably have little room for stupidly expensive projects to fill a niche market.