I can't believe how much the ending threw away the excellent work that had been done throughout the rest of the game. Seriously.
One thing that had already made me a bit grumpy was that I didn't know that multiplayer would play such a role in the single player game. I'm not a fan of online play, yet because I won't play it, the readiness of the fleet will never go above 50%? How is that fair when I've invested so much time into the previous games that went nowhere near the multiplayer? It directly affects the outcome, though to be fair, even the 'perfect' ending is pretty much the same as the others.
I was also disappointed that all the hard work that went into uniting the races, and scanning all of the various planets and systems all sort of goes down the toilet with the three vaguely similar bad endings. I would have thought that the final scenes would have been a bit more like the epic suicide mission in ME2, except on a much bigger scale with all of the different things in play. It just all went a bit Matrix Reloaded with the introduction of the catalyst boy.
How come the three choices at the end are the
only choices we get? Why isn't Shepard making an impassioned speech about how the cycle is finally being broken, and that the races should be given a chance? The level of cooperatrion amongst the aliens was unprecedented, but apparently it didn't mean anything. These are the only three choices, and you must pick one of them! Why can't I just ignore him and rally the troops for one last push?
I chose to destroy the reapers, as I felt that this was the closest in character for Shepard. The notion of losing all of the synthetic lifeforms was a bit dire though, especially after everything I did for the Geth in ME2 and 3. And of course EDI, one of my favourite squadmates in the game, is also synthetic. Is she a gonner too?
I couldn't choose to control the reapers, as that just came across as indoctrination. The Illusive Man needed bringing down (I enjoyed killing him!), and I wasn't about to step in his shoes. The merging of organic and synthetic beings sounded like one of Deus Ex's ending from years back, but still sounded a bit too pro-reaper. In fact all the endings were a bit dystopian, which seemed like an odd turn to take at the last minute, when the Mass Effect series had never been in that style.
I didn't understand how the Normandy was flying away from that shockwave, when not long before it was in orbit of Earth. Not only that, but Tali and Liara somehow get out alive, despite just being in the mad rush to the teleportation beam in London that saw deaths left, right and centre. They didn't come up to the Citadel with me, but they didn't die either? Where the hell did they go?
Seeing the Mass Effect relays all being destroyed left me wondering for the safety of the different aliens (well Tali in particular) that survived after the Normandy crash. Oh, and of course the enormous fleet that was still in the Sol system - are they all trapped there? The FTL drives aren't the way to travel great distances in the ME universe.
There, I think I got it all out.

I wasn't searching for a super duper happy ending or anything like that. All I want is for there to be a better choice for Shepard, or at least explain what will happen for each one properly.
The rest of the game was truly amazing - one of the best times I've had playing a game. I was so immersed throughout, meaning getting teary eyed at seeing particularly poignant deaths of Mordin, Thane, Legion and even Miranda who I was never keen on.
By the time I was at the makeshift barracks, about to launch into the final push, my stomach was churning. I couldn't believe how tense I felt after saying my last goodbyes to my squad, and to whoever else out there who was still alive. In particular, seeing Garrus trying to be tough but still letting on how scared he is, was very effective. It made the final battles all the more emotional, especially since I knew it was all coming to an end soon.
Everything else was so well done that it's no wonder that a duff ending knocked me back a bit. All of the emotional investment wasn't paid off properly.