Endings were blindingly unoriginal which is probably the only thing I can objectively mention as a flaw. Deus Ex all over again and I only wonder if there is a hidden ending in ME3 where the whole Normandy crew dances on a dance floor with music and lights.
I have been reading again and again that choices you make during ME1 and ME2 don't matter when faced with the ME3 ending. I agree, since it seems that all the effort went null with relays gone and galaxy crippled. However, I took a step back and looked at the whole Mass Effect 3 as an ending itself. Imagine 35 hours long (+-) ending scene where you are told how the decisions you made before affected the the final battle (but through an interactive form of a game). Not the outcome of the battle, but the way the battle happened.
Therefore you don't make decisions during ME1 and ME2 to see different endings at the end of ME3, but to see different Mass Effect 3.
I picked the control version, since Synergy wasn't available for whatever reason, maybe because I left the Collectors' Base up (it seemed as a valuable war asset after all even though I was against using humans for fueling). For me it was logical since I was told Mass Relays would be done. But with the control over Reapers and their logistics power I could help other civilizations settle in. Destroying was simply too brutal and I wasn't ready to loose all the technology, EDI and Geth.
For me the Control ending is the best and it satisfied me.
The endings were, from time to time, illogical and probably badly narrated. I got hit by the red beam with Garrus and Liara in my squad, but I saw them both leaving the crashed Normandy. Without any sort of explanation. Also what the hell was Normandy doing there?
I only wish Obsidian had done the ending (or the whole story), looking back at Mask of the Betrayer, which was amazing but still bittersweet or at both Fallouts. If there was a sliding show with Stargazed telling what happened to each civilization I would be totally happy. Hell I went through the whole Fallout 2 just to get New Reno in line since I did pick the wrong family there.
Endings could have been so so so much better and I'm shocked more time / though hasn't been put in them. The sense of completion or even bittersweet satisfaction is somehow lacking.
An ending we could have gotten (my idea):
*Shepard sits next to Anderson after The Illusive Man dies and we hear their conversation*
*Anderson's head drops and we see Shepard looking at her / his injuries*
*Hackett calls that nothing is happening, so Shepard gathers all remaining strength and hits a button on the console*
*The screen goes black slowly with Shepard breathing on the ground exhausted*
*Cut and we see a blue light emitting from the Citadel disabling all Reapers, but leaving Mass Relays intact*
*Shepard is lying on a sunbed on a beach without any injuries, drinking with her / his love interest (or alone) without anyone else around, both are chatting and relaxing and look happy. Garrus is slowly walking past them on the background with reasonable distance*
*The screen slowly goes black again*
*Sad music starts playing* *We see a hospital room (similar to one on Citadel) with located in London, Big Ben is clearly visible in the background through the large glass. Shepard is lying on the hospital sick-bed severely injured, blanked covers half of her / his body, head is bandaged. The love interest is sitting on a chair next the sick-bed, holding Shepard by her / his hand.*
*The camera steadily back up and away and we can hear the hospital beeping slowly going flat, implying the beach was only a dream*
*As the camera backs away, there is a man on wheelchair (also severely injured, but stable) in a corner, watching Big Ben*
*When the hospital equipment stops beeping a doctor reluctantly comes to the wheelchair, we notice Admiral Anderson as he looks up and behind him, nodding at the doctor. The Doctor grabs the wheelchair handles and gently walks off the screen while pushing the wheelchair*
*The hospital equipment is still making the flatline sound and the screen goes black*
Why didn't we get something like this? Very, very grim, but at least with a sense of completion.