The main problem with the current endings that it's almost impossible (game technically, and not to mention the novels) to create a sequel which fans want the most. The only possible way to continue and expand the universe of ME if BioWare canonize the ending but then what was the point of 3 (or with the refuse it's 4) options?
My other main concern is that when you play through ME1 and ME2 you'll get a clue that humans are important most probably because of they genetic diversity because that's unique in the whole galaxy. Probably that's why the collector's took humans and turned them into a Reaper larve. Even Harbinger himself admits it in ME2 that humans are so important because of they genetic diversity. YET there's not even a single word about it in ME3 and not to mention about the ending. We're just like the other species only difference that we have Shepard (yes we have Shepard and Shepard is not you. Because they filled ME3 with so much auto dialogues that you rather feel you're observing a character rather than controlling it. And also the stupidly simplified conversation wheel...). Big deal, we're no more important that the Batarians or the Vorcha. Do you remember Mordin's recruit mission in ME2? A virus that effects all species except humans and vorcha? And it was developed by the Collectors who're the puppets of the Reapers (especially Harbinger).
Also Harbinger doesn't even speaks in ME3 and what everyone wanted and waited since ME2 was a final boss encounter with Harbinger. At my first playthrough when Anderson mentioned that several Sovereign class Reaper heading to Earth including Harbinger I was like "yeah finally, a decent boss fight and after that I can finally question Harbinger... probably". But NO. He just lands shoots laser, shoots you, flies away and you allready know what happens afterwards. That's just bull....
In trilogys the second installment is all about foreshadowing, hinting of what will happen in the last installment what awaits you. ME3 especially it's ending is totally goes against this and ignores EVERYTHING that has hinted before not just in ME2 but in ME1.
That's why I hate the endings!