The problem with ME3, is rooted in ME2. Say what you will about ME1 (I'll agree to most about everything) but the such drastic changes that ME2 suffered as a result, upsetting the tone to which the franchise couldn't handle.
ME2 is a complete 180 difference in tone and direction that ME1 started the franchise out in. By ME3, having being pulled in both directions already from ME1 and ME2, felt paralyzed as a result and suffered in the end.
[Yet; I will admit the best to come from ME2 is Legion and Mordin]
ME1 is best described as an "open world space opera / mystery".
ME2 is best described as a "closed corridor space action adventure".
I think fixing ME3, requires fixing ME2, in which I mean completely rewriting the script.
ME1 set the tone that Shepard is a badass who can get anything done, yet only his small group believes in the "Reapers" [The Council dismissed that claim].
ME2 would have set a stronger tone if the game stayed on that same focus. Shepard is still the first and foremost bad-ass Spectre, but his higher ups are growing increasing frustrated with his(/her) fixation on the Reaper issue. The only reason the Council keeps Shepard on the pay-role despite his child-like obsession with the "Reapers" is his ability to "get it* done." [*it being ultra classified missions.]
Between Spectre missions (of straight up bad assery) ME2 constantly puts Shepard into contact with ancient Reaper artifacts which continues his downward spiral of spiritual insanity. Shepard goes mentally "crazier" but gets combat "better" [yet you still are still in control of his Morality -- that never changes].
This sets up the stage for Arrival perfectly, and of course by ME3 hits, Shepard finally feels that euphoric validation of finally being right, but is in such in a mental state of fragility (due to Reaper mental manipulation) nearly is unable to stop the Reapers. Despite the man everybody now looks to (for finally being "right").
I'm on the fence if we should have a one final show down ending: (Which is noted below because.. hey.. as Bioware showed, 1-2 endings is much cheaper [used in all manners of the word cheap] then making up 4-10 endings.
For which, the Crucible is a galaxy wide transmitter with the ability to rewrite the Reapers. But the reason nobody has ever had a chance to build/use one before, is because nobody knew of Reaper programing before, except until now, when Nazara provided the Geth part of his code. [Nazara's real motives were to only used the Geth, and then eradicate them when they helped open the Citadel's relay... but we know how that turned out for him). Either by force or by friendship, the Geth give you the code to rewrite the Reaper Programing code. Due to damage, the Crucible requires a human to fire it. That human will be Shepard. The ending either boils down to having the Reapers help rebuild, or have them all fly into the nearest sun/blackhole.. forever ending their influence (short of the Mass Relays).