Frankly, the most they ever need to acknowledge DMC2 is to have Lucia show up in a cameo of some sort to establish that the next game takes place after it.They need to address DMC2 sooner or later and while Vergil was not part of it, doesn't mean he can't be made in some way one of the wheels that set the events of the game in motion or that his fate will tie in to events of that game's possible sequel.
Arius could have come from Fortuna originally, and left island as result of something happening while Vergil was there. Agnus' research, focusing a lot on Yamato and pieces of Nelo Angelo's armor, could have served as basis for creation of Secretaries. And so on.
The overall story of that game was fairly inconsequential, even with the whole "Dante killed the metaphysical embodiment of despair" thing.