I like theories, and reconciling the differences to allow for a smooth transition would certainly be nice :), but to counter a bit:
We were indeed about to leave the system at the end of M2, or stay to work our tan.... We had done what we needed to, had found answers among the ruins and brought back the S'pht'Kr - we had won.
Durandal said Tycho was dead back on Fatum Iustum Stultorum, yet now he assumes the nearby ship is under Tycho's command. Unless that idea of the universe having forgotten its own rules has also affected Durandal's memory, that's a little odd.
We were presumably meant to be teleported back to D's ship at the end of M2, and we have observed that the M2 final screen makes no mention of what happens to us, but conveniently skips an awfully long period of time. The one part I really do like about trying to reconcile M2 and Moo is that that final screen makes a lot more sense after Dura-Thoth releases us from service in Aye Mak Sicur. I like to think that Infinity is contained between All Roads and that M2 final screen - as in the Aye Mak Sicur timeline leads to it, rather than it takes place in the intervening 10,000 years :), but I think NCM is in a separate timeline, and I think that the fact that what Durandal says seems so out of kilter with M2 is the best sign of such to the player.
Of course, all of that leaves us without a failed ending for the M2 timeline, and without a rest of timeline for NCM, but we've got a lot of gaps, so I'm not sure we can be too picky. Maybe All Roads should have been followed by an Electric Sheep?
