I've started thinking that myself.As for new Enterprise, I think they should go the Netflix route with the "Prime" universe Trek and Enterprise, if Enterprise is even in the Prime universe. I wonder if Enterprise is in the JJ Abrams universe after what happened in First Contact and Prime Spock fell into that universe. Then the episode "These are the Voyages" and Trip Tucker's death can be explained away as being in the alternate universe.
For the MU two-parter, since we know so little of Interphase then there is nothing to say it couldn't cross realities.