It's actually the total opposite for me. Religious aspect aside, my Shep fits very well with Cap. Pretty much the same strong paragon persona where he will accomplish the goal no matter what but will do anything in the realm of possibility to save people.
Oh my Shepard saves who he can as well. Unless they're morons and/or actively antagonistic. Or there's a really good reason not to. This is where the conflict would come in. I let the Council die, I pushed that merc out the window, I shot Elnora and Brooks. Cap would definitely have issues with that.
Possible Spoilers, if any....
The info is very intriging, and I'm excited for it. But "if" the plot is set in the future, how is BioWare going toallow the game to vary depending on the players' end results in ME3? Wouldn't it be like making three different games at one time? And why is there a search for a new home for humanity if the war was won, in three different ways? Or is this all something completely new where the story of Shepard and the Reapers never existed? E3 cannot come sooner....
They won't. That's the point, to get away from the trainwreck that is ME3 without canonizing anything. They can't possibly account for everything in one game. So fresh start. The Ark may have been a contigency measure, launched during the war (or maybe even before) to escape the Reapers. The war happened but we don't deal with it because we're elsewhere. At least that's the theory.
A fresh start without invalidating what we were left with. I didn't think it was possible. But if this is true it may actually bring me back into the fold. Provided none of the propagators of "art" are still around doing anything other than fetching coffee.