It would have been great to have the final missions difficulty be altered by your resources. An example includes your about to go up against a large amount of banshees, then a platoon of Geth primes come in to fight them (That'd be cool, Machines vs Demons....)
Same goes for your fleets and such, the Turians punch a hole through the reapers while the Quarians defend the crucible etc.
It'd be the best ending to the game franchise, all it needed was for our choices to matter, not be part of a big addition problem.