That 3.9 million includes a lot of versions of the same games. Since the first Phoenix Wright's release in Japan in 2001, the five games have been released on Game Boy Advance, PC, DS, mobile phones, iPhone, and WiiWare. The four Professor Layton games have only been released once each on DS, with a couple of original games on Japanese cell phones. However, Layton has Nintendo marketing behind it in the west, with Nintendo pushing the puzzle games to audiences beyond the core gamer set.
Even though this game announcement was beyond effective with fanboys (we know from, um, reading comments and not personal experience at all!), the two companies still have audience expansion in mind. "We feel that by drawing upon the strengths of both series, this collaboration will bring new, casual game players to the adventure game genre and into the world of gaming in general while strengthening the value of the two brands overall."