so, it took me a bit, but I finally beat Mass Effect 3. And since everyone is up in arms about the ending, I figured I'd come by and add my two cents.
For reference, I got the Good Control ending.
Honestly, I don't understand all the complaints. The ending was most certainly not perfect. I certainly have some problems with it. The lack of any real last boss is something that I personally dislike. Harbinger getting to live, and not just getting to live but not even really appearing at all throughout the entire game except for one brief moment near the end to shoot laser beams at us. I understand with other endings he would've died, but I still would've preferred an actual confrontation with him somehow. Especially since he had such an awesome voice. And to top it all off, the entire bit with the Normandy didn't really make any sense at all (why was it flying anywhere and why were my squadmates on it? They should've been on Earth. Especially Garrus and Tali, who were my chosen squad, and who I assumed would've died in the charge towards the beam of light and Harbinger, but who were seen exiting the Normandy, or at least Garrus was).
That said, I don't understand a lot of the complaints. Not every ending needs to be happy. Hell, the game repeatedly brought up the need to do whatever it takes to win, and how risky everything was. For Shepard to die at the end was fitting. The mass relays being destroyed will forever change galactic society, but at least galactic society still exists instead of going extinct. These were the costs of victory.
Even with the mass relays gone, there's still FTL travel. It's slower, true, but both ME1 and 3 via the protheans showed that long-term stasis/hibernation is possible. And, in my ending at least, the Charon Relay was only damaged instead of outright exploding, meaning it could theoretically be repaired and copied to rebuild new mass relays if people really wanted to. It would take time, but again, that's time that actually exists now.
In regards to what happens when a mass relay is destroyed, well, there are multiple ways of destroying everything, and I like to think that the method with which they were destroyed wouldn't have quite the same impact as ramming an asteroid into one. But I guess that could be argued as either a plot hole or a lot of systems being wiped out (systems under reaper control to begin with and thus already in bad shape).
About how much my choices impacted the ending, well, that's no different from ME1 or 2. In 1, the only choice that really mattered for the end was save or sacrifice the council, and arguably Anderson or Udina for councilor (I'd argue that choice doesn't matter since it only changes a line or two, has to be remade in 2, and is thrown out the window in 3). In 2, the only choices that mattered was destroy or save the collector base (both of which result in the same cut scene, just a different Illusive Man conversation) and whether or not you do your squad's loyalty missions or not. Hell, the choices you make during those missions don't even matter for the most part so long as you do them. In this regard, I don't see how 3 was expected to be different. With all the hundreds of choices that are made throughout the game, referencing them all costs a lot of writing, time, and development resources, and then you have to choose which decisions to reference and either way someone's gonna be disappointed. In the end, I cured the genophage. I know that was important, and people throughout the game referenced it. I don't need it to be included in the ending for me to know my decision mattered.
The Stargazer part was just... weird. Don't even know what to think of that. I view it as neither good nor bad, just odd.
Ultimately, the ending was not perfect, it was flawed, but it wasn't even close to being one of the worst endings I've seen, it certainly wasn't bad enough to lessen my enjoyment of the game itself, and I have no regrets about the time I've spent playing and don't view the franchise as being any lesser for it. Hell, it was at least good enough to stir emotions throughout the whole thing, from the showdown with Illusive Man, the last conversation with Anderson, and finally watching my Shepard sacrifice herself to control the reapers, and that's more than I can say for a lot of games, and movies, and books, and TV shows, etc. So I'd go so far as to call it a fairly decent ending at least. Even if specific details left something to be desired, it hit all the right emotional chords.
Honestly, at this point I think it's too late and that it's probably coming anyways, but I REALLY hope Bioware doesn't give in and change the ending. I don't think it needs to be changed at all. That's just like George Lucas going back and changing/ruining the original Star Wars movies. You don't change art. You can critique it, give it advice for making the next one better, for improving, but you don't go back and alter a finished product. Revisionist history sucks. If we get a new ending, it just feels like caving in to a bunch of whiny, spoiled brats. Especially since even if the ending gets changed, there's still no way it'll ever satisfy everyone. Though, as an aside, if it DOES get changed via DLC, the DLC better at least be free, because if it has to be paid for, that would be extremely sleazy and would basically be admitting that everyone hypothesizing that you'd have to pay for the 'true' ending would be right, and I really don't want them to be right. Something that sleazy would forever taint Bioware's otherwise good reputation.
Finally, I don't buy the indoctrination theory. It's interesting, and there's definitely some pieces and hints that support it, enough that I'd say it's probably a valid interpretation of events for people who want to see it that way, but I'm personally not one of those people, and the pieces don't fit together well enough for it to be fact/the only way to see it.