Although it might be that no choices carry over at all, given how distanced, both in time and space, the new story seems to be to the original games.
Unless this is a solid reboot with an unspecified but different outcome to the Reaper War (or, one where the Reapers never invaded, as difficult as that is to imagine), then there would be significant differences to the base of the game.
If you select Destroy, then there is a measured possibility that Cmdr Shepard survived the war and may also be a significant post-war political figure. Additionally, the Geth would be extinct (possibly the Quarians too, as the destruction of the Geth would have made re-inhabiting Rannoch a lot more difficult). If you select Control, then familiarity with the Reapers as the 'troubleshooters' of the galaxy (as worrying as that is) would be a routine part of life for a galactic citizen. If it's Synthesis then all of the Milky Way-origin characters are fully-blended biomechanisms, as much synthetic as they are biological.
The difficulty of implementing three different starting conditions for the Milky Way-originating characters would mean that it would be somewhat simpler for Bioware to select a 'canon' ending for ME3 and go forward from there. Simpler technically; in terms of fan reaction, it would be a can of worms.
Honestly I don't think they went pure fanservice soft space porn on us. It's probably just how it ended up rolling along. I sincerely believe that we'll get decent writing (They did damn well with DA:Inquisition and ME3).
. . . As well as all the azure you can shake a quad at. . . >_>