Couldn't be possible for BioWare to let you "customize" the world before starting the game like in ME2?
Of course it would be more expensive but they could just try to minimize the effects of the decisions. Like if you chose Synthesis, just give everybody green tech eyes (shouldn't be troublesome, is just texture) and do some minor changes in dialogue.. something like that.
I think everyone becoming cyborgs would lead to quite a different future than the other endings. They should pick an ending and just go with it if they even bother caring about any of that.