I know I'm probably the odd man out here, but for me, it didn't fall apart with starchild, or the Reaper's conflicting messages (though they certainly didn't help matters). For me, the big unraveling part was Cerberus (ME2 to ME3)
In six months, (however long Shep was under house arrest) I'm supposed to believe that Cerberus suddenly transformed from this small, under-the radar, rogue black ops organization to all of a sudden being this galactic powerhouse that is capable of not only challenging the Salarian, Turian, and citadel-based militaries, but often times completely obliterating them. In almost half the side missions (and some main ones) if Shepard hadn't showed up, Cerberus would've somehow dominated.
A base on the SALARIAN HOMEWORLD? Too easy.
Operating with impunity on Tuchanka? Cakewalk.
Making an experienced Turian platoon look like a JROTC unit? Check.
Taking over the seat of galactic government during wartime? No sweat.
Taking over the elite mercenary/pirate hub of the galaxy? Not a problem.
Going toe to toe with the Alliance Navy at Kronos Station? Bring it.
And its not forgiven because they say TIM turned to indoctrination to bolster numbers. The amount of soldiers, gear, top-line weapons, biotic-capable individuals, mechs, and spaceworthy warships, (not to mention constant access to intel better than what the STG could acquire and a seemingly inexhaustible list of double agents and contacts) simply doesn't add up for me. Even if they somehow had all this stuff stored away for a rainy day, there's no way that you trained an elite military this size in that amount of time.
But anyway, you get the idea. I think it falls apart when they portray Cerberus as an equal (or greater) threat than the primary antagonists that have been set up for the entire series. Don't get me wrong, I understand the need for a secondary villian, and I like the concept behind Cerberus, it's the execution of that concept that I take issue with, more so than the ending.