Lord Cutler Beckett, it's just good business. Or, as Capcom's Seth Killian explained on the Capcom-Unity forums, releasing a downloadable version of Capcom vs. SNK 2 could be bad business. In a lengthy response to a call for the game on PSN, Killian gave several reasons for not re-releasing Capcom vs. SNK 2; all of them centered squarely on business. Among other things, the audience for the game is less sizable than that of Street Fighter and Marvel vs. Capcom 2, meaning a Capcom vs. SNK 2 port probably wouldn't be worth the money and resources Capcom would need to spend.
Killian noted that even if sales covered cost, placing developers on the project would mean removing them from others, like Super Street Fighter IV. Killian put it simply, saying, "When fan service becomes a black hole for time and money, that party gets ended pretty quick."
Another explanation, according to Killian, is that Capcom doesn't want to flood the market with fighting games. He suggested that most gamers only buy one or two fighting games a year -- thanks mainly to the amount of time it takes to master them. In other words, releasing too many games could dilute the sales of all of them. Besides, we all know that what Capcom should be working on is a new Darkstalkers.