Although info didn't come from the Activision presswire, IGN has confirmed that the wise-cracking merc will be part of Marvel: Ultimate Alliance 2 (DS, Wii, PS3, PSP, Xbox 360). I'm guessing that it would be Deadpool's strong performance and sheer coolness in the first Ultimate Alliance that brought him back. Let's just face it, he's way too cool.
Info came from a Marvel: Ultimate Alliance 2 ad included in the newly-released X-Men Origins: Wolverine, where Deadpool was seen alongside the already confirmed characters for MUA2, such as Spidey and the Hulk. Also worth noting is that he'll be coming in his classic look, and not the X-Men Origins movie look.
More info for Marvel: Ultimate Alliance 2: