I have to imagine there was some... internal bioware issues with either scheduling/ writing, or -something-. They took such care with the endings and final missions for the first two games, it really, really doesn't add up that they didn't stick the landing on this one.
The plot falls apart completely and its a giant turd, so I'ma chalk it up to EA being jerks and somehow poisoning the well, maybe making them worry about pay-to-play forced multiplayer microtransaction bullshit and not finishing their damn single player game.
One (of the many) things that really annoyed me, was that at least in ME2 (EA influence not withstanding), it actually -mattered- who you brought on your squad, and what tasks they were given. you had an actual sense of being on a difficult suicide mission, and a crack team working together and making it happen.
This game was just you running around collecting a bunch of numbers to throw at the enemy. How much more interesting if you had to make actual -decisions- with the finale? Tough decisions about how to use all those war assets you had been collecting the entire damn game? Send in the Krogans as shock troops? Suicide the Geth fleets first? That kind of thing. Make it effect the outcome and how you play the final missions.
Illusive man, built up as the master strategist and always one step ahead, leader of an entire army, shows up to the final confrontation by himself with a handgun? And then you just.... talk him into suicide.... good effing gravy.