Well Marvel actually did it. They added Agent Coulson to the Marvel Universe and also made Nick Fury more in line with the movie and Ultimate Version of the character. I'm not surprised they actually did this and at least it wasn't too convoluted. The new Nick Fury is actually the son of the original. And Agent Coulson is now just part of SHIELD. They could have done much worse but at least the original Fury is still alive and out there for now.