The peek-a-boo shooting got tiresome, but I agree was a good change from the drama. I don't see what's wrong with mixing the two, just have the PC's skil affect the player's aim, scope sway, reticle spread, etc. Nice abstraction.
As for the timed dialogue, I doubt they'll give you 5 seconds to make a choice. AP gave you a fair amount of time (never clocked it). Also you have the NPC's audio and the dialogue choices in ME aren't that long so accessibility (the actual version) shouldn't be a problem.