Pretty simple.
1) During the raid on the Illusive Mans station, it would turn out when Shephard confronted him that he ultimately wasn't indoctrinated and under Reaper control, and that he truly believed he could control the reapers. While Shephard and him are arguing, the Reapers suddenly bust in from FTL, catching the attacking fleet between the station and themself. The Illusive Man at this points try to exercise his control plan over the reapers while Shephard battles Kai Leng. The Illusive Mans plans fail, and he breaks down as the Reapers bombard both the station and the human fleet. At this point Shephard has the option to either enlist his help or kill him and take over Cerberus.
Why?
Because i feel that Indoctrination has become a bad cliche of the series. It would be refreshing for once to have the game fool us into believing someone has been indoctrinated (because until that point, everyone and their dog has been), only to reveal that for once it was simple uncontrolled ambition that was the reason.
2) The Crucible is simply a weapon that can kill reapers off relatively easily. Reapers are never explained and the idiotic crucible child doesn't exist. Cleansing the galaxy of reapers would still be a slow task that will take years to finish, but with the Crucible it's ultimately going to happen, and Earth is still saved.
Why?
"This isn't rocket science. Mysteries lose all the appeal the instant you explain them."
- Yahtzee, Condomed 2 review
Like Sovereign said in Mass Effect 1 "We... simply are." Point being that i feel that the Reapers was an enemy that would have been better off staying (mostly) unexplained. The devs should have picked up on this little cue rather than explain the reapers with some kind of godly entity.
3) Shephard needs an actual Battle with Harbinger.
Not giving us any Harbinger in ME3 (with the exception of running towards a portal while he is throwing pot-shots at you) is the worst tease I've ever experienced in my life. He has been set up as such a massive influence and villain in ME2 and is pretty much non-essential in ME3. Terrible storytelling right there.
4) More epilogue containing Shephard (alive).
Why? Well if anyone here has played Baldur's Gate 2 and romanced someone, you should know then that when you finish Throne of Bhaal, you get an epilogue containing the continued life of you and your love interest.
This is one of the things Mass Effect is sorely lacking. Why go around romancing your crew members, when you aren't gonna see an outcome or a future together anyway? Many fans have expressed disappointment with the fact that they were really hoping to see how Shephard and their love interests would continue their life (for example, watching a cutscene of male Shephard and Tali building a home on Talis retaken homeworld).
Also, this goes hand in hand with us needing more endings with Shephard alive (and kicking). Now, normally I'm not the guy to claim that every game should have happy endings. The Galaxy at War system, however, changes that.
Since it's a way to quite clearly measure your progress against the reapers (War Effort), it sets up the expectation that if you work off your ass hard enough, do all sidequests, and get as much readiness rating as possible, you can see a (semi)good ending. But after you've worked your ass off to maximize all of this, the game kicks you in the nuts anyway and gives you a shit ending. Not acceptable. Period.
Oh yeah, and the Indoctrination theory that so many people used to fantasize about can take a ferry out of this world. It was a terrible theory before Extended Cut was released, and I'm happy that Extended Cut put a bullet to it.