By Tartilus of the Bioware forums (I am not he;I just thought this should be shared)
I think it's important for us to consider that, at some point, a community manager is going to have to explain our thoughts to any number of developers, and accordingly it's important that a succinct list of our concerns with the ending is available. Those concerns are numerous, and here are the ones I'm familiar with so far:
1. The endings are extremely sad. This is a much-maligned criticism by individuals who associate depth with the perceived darkness of the endings, and that may or may not be a fair point. Regardless, it stands as obvious that many people were hoping for an ending which proffered some hope beyond that available in even the 'happiest' of endings.
2. The endings contain plotholes. The escape of the Normandy and the teleportation of her crew (including the formerly deceased) are the most obvious, but the lack of sufficient explanation regarding the Catalyst's efforts and origin also makes many of his/its motivations bizarre and unsatisfying.
3. The endings fail to fit in with the broadest themes of the series. Slightly different from 1, this criticism notes that the story of Commander Shepherd has always been a story of achieving the impossible with the help of a close crew and rigorous preparation. The endings as offered do not incorporate the crew, do not change significantly in response to your preparation, and while perhaps technically constitute doing the impossible, fail to meet even that low bar which is a solution that does not have an inevitable cross-racial holocaust and galactic dark age as its result.
4. The endings lack variety. This criticism can be directed at both the artistic and story aspects of the ending ? the results of the ending decision not only vary little (at least, and this is important, on a scale which is important to our experiences in the game), but the resulting cinematics have only minor differences, and the various sub-endings result in changes so small as to be entirely unnoticeable. Consider that some way could've been contrived to make the Synthetic option differ from the Control option in a fashion greater than a change in the color of the 'light' and a different Texture for Joker in the games final seconds.
5. The mechanics of the ending are not appropriate. Without repeating the various criticisms as regards the ending closely mirroring Deus Ex's, the culmination of the story with a game-show-esque approach to saving the world very much fails to be satisfactory, especially when Mass Effect has otherwise been about the integration of choice into the experience
6. The endings lack dependency on the player's choices prior to the last five minutes. This is important, because the entire rest of Mass Effect 3 was about reacting to previous decisions; consider that, provided one is able to fill the 'war asset' bar in a satisfactory manner via some other means, the decisions in the third game serve no purpose to explain, shape, or enhance the endings. This seems contrary to the spirit of the other 95% of the experience.
7. The endings do not make sense given the character of Shepherd. As has been state elsewhere, we are playing some heroic badass who has otherwise talked down to, shrugged off, and inevitably defeated everyone who threatened, cajoled, or otherwise tried to force him to do something he didn't wish to do. In the ending to ME3, this character offers no rigorous questioning, no protests, no counter-arguments, no discussion of any kind save a resigned sort of death-march which could not be more contrary to his character. This is distressing.
8. The endings have implications, perhaps unintended, which seem to ruin the ME Universe. Admittedly, many of these implications could be avoided, but the lack of contrary evidence fosters a suspicion that these matters were either otherwise not considered, or supposed to be generally acceptable. Indeed, they might even be, but only with proper elaboration, of which there is none.
9. The endings fail to provide closure. There is, as a diagram that is floating around illustrates, no falling action. No conclusion. I do not know what happened to my squadmates ? I do not, for reasons that may be bug related, even know which of them is alive. I do not know what happens to the universe, or to the people I've saved. I do not know how I'm remembered, or if any of the terrible things mentioned above actually happens. There almost could not possibly have been less information provided regarding the ending of the game, and that is incredibly distressing when the intention was to wrap up a series that had otherwise displayed all the signs of excellency and had a fond place in our hearts.