Just my 2p:
I like the concept of the endings. I thought they were interesting. And it also makes sense to me that in the end, after everything you've done, all the choices you made, it doesn't actually matter. All that matters is that those choices got you to the crucible - like godkid said, the first organic ever to be there. I even thought it was interesting that TIM turned out to be 'right' all along - controlling the Reapers could be a better option (though that does depend on what you did once you controlled them - and that's never explained - big difference between controlling them to get them to leave us alone and controlling them like TIM wanted).
I don't even mind Shep being a bit out of character at the end - I mean come on, you've been hit by a giant laser, been controlled by TIM, quite possibly shot a close friend and just the fact you're even standing is a bit of a miracle. The game as a whole made it seem to me like Shep was just losing the will and being ground down, especially in the later scenes (femshep at least sounded horribly weary and hopeless after that final nightmare), and by that end point - just 'do you know how I can stop it?' - that's all that mattered.
What I missed out on was the epicness of the final scenes. The space battle. Not scenes of random soldiers cheering, but my comrades fighting, crouching behind cover and looking up with amazement and relief as the Reapers 'splode/fly off/go glowy green. Those were the people I invested in. There was so much epicness throughout the game - I already admitted to myself after watching it that the ending would probably never beat the Tuchanka quest ending for me in terms of sheer awe - and it's sad that the last few scenes just seemed so very rushed. Why did my armour/weapons disappear, but later if you're lucky enough to wake up it's magically back? How could TIM control Anderson when he isn't full of bits of Reaper tech? What the hell is the Normandy doing and why are my squadmates suddenly on her? And of course, the pure lack of explanation in the conversation with godkid - if you're going to add an explanation, try to make it one that actually EXPLAINS, or just leave it as 'we are too advanced to comprehend'. ME1 might have been a bit much grind at some points, but that ending was pretty epic - the space battle going on above while you fought Saren below, all tying in to create one amazing battle that gave you a personal role as well as using the whole galactic fleet. ME2 brought in the mechanic of choices and allies affecting battle outcome, which I thought would be how they'd use your accumulated EMS. I have to admit when they talked about getting to the Citadel while the fleet fought above Earth that THAT would be how it played out - you'd be fighting to just activate the Crucible, and the allies you accumulated and choices you made during the battle bought you that time, with the two battles creating a cohesive story - you on the ground and your fleets in space. Instead EMS just got ignored, which was a bit sad.
Lastly, some kind of epilogue would have been nice. It didn't have to be massive. Perhaps just a scene for each species - Wrex and his 'wife' (or whatever she is) with a clutch of babies (or them looking at a stillborn, if you screwed them over), Tali (and possibly Garrus, d'awwww) building on Rannoch with a bunch of geth helping if you managed that peace, maybe the Alliance unveiling a monument with your crew there (not a statue, too corny lol - but something with the names of all the people who died, with yours and Andersons right at the top). Hell, even just knowing that anyone SURVIVED would be useful, and I don't count the final Normandy scene as it lacks any explanation that makes sense.
All most of us really want as far as I can tell from reading all this is the plot holes fixed, a more detailed explanation, and some closure on the characters and events were interacted with. Sure, some people want their happy ending - personally, I don't care for my Shep to settle down and have babies and after all s/he's been through in ME3, the personality changes taking place, I'm not sure s/he could - but lets at least see what remains of our crew mourning Shep, see something about how s/he influenced their lives, especially the LI as many people are very invested in that. Even better if it can be left a little bit ambiguous - a little room for imagination is a good thing!
Ahhhh, that was longer than I'd planned. My mate hasn't finished the game yet so I haven't had a proper chance to discuss