Well it's all about how much you question things; how much you need to make sense of them. Fans of Science Fiction tend to run a bit more along this line, and lets face it, up until the ending of 3 this series was the best hard SF game (FYI hard SF is an exporation in how a specific technological innovation changes the human condition) ever. Fantasy fans really can't be that way since they have to buy into a world where a few mumbled words and gestures conjures a ball of plasma simply because the writer says it does.
Now I've met several people who didn't have the issues I had with the ending, and to be honest we disagree regularly on stories. These are people who say Captain America Winter Soldier was amazing despite the half assed plotline about the dangers of relying solely on the government for protection and disliked The Amazing Spiderman 2 despite it's brilliantly executed expose on the motivations of people. In essence if you give them flashy action and lots of explosions and they are happy. If that's good for you that's fine. Some of my closest friends are that way and they've learned not to ask me what I think of a movie unless they want me to analyze it piece by piece.
The same is true of the ending of ME3. I haven't even played it since the DLC that supposedly 'fixed' the ending yet the flaws are still fresh in my mind. It was a sad sad thing they did to a story that had so much promise.
1) The Godlike Star Child; We are confronted with an avatar that originally didn't identify itself. It merely stated that it created the reapers to destroy organic civilizations because organics will inevitably create AIs that will kill them. This is akin to me telling you 'you're going to die someday so I'll just kill you today'. The logic escapes me. Also you don't put gods in hard SF; that's too akin to adding magic. This explanation also does not explain the StarChild's motives. Nothing defines what IT is getting out of this. They'd have been better off saying it was psychotic and got off by feasting on the flesh of sentient beings. Now nothing says the StarChild can't be lying, but as the story teller bioware does need to give a rational (emphasis on rational) reason for why it does what it does.
2) The AI Star Child; And then, in a half assed attempt to explain away the flaws bioware reveales that the Star Child is an AI which boils the excuse for the reaper's actions down to 'someday AI will kill you so I'll just have my AI's do it now.' Makes even less sense.
3) The Godlike/AI Star Child; In conversation with the Starchild it very pleasantly informs you of your choices (kill it, the reapers, all computers, and the mass effect relays/ kill it and take it's place somehow destroying the mass effect relays/ merge the reapers with organics somehow destroying the mass effect relays). It sounds resigned to its fate of having its entire existence in Shepard's hands. But does it really? Because if you shoot the StarChild (as many disgruntled Mass Effect fans did in frustration) it announces that the cycle will continue and shuts the crucible down. This begs the question of how the crucible was ever supposed to be a threat to it as it clearly had complete control over the device.
4) The Mass Effect Relays; The relays are the very essence of this universe. It is through them that the player explores the galaxy, its through them that all the advanced technologies you see and most of your abilities were engineered. The mass effect relays are what seperate this universe from ours. Destroying them is on some very basic level destroying that universe in the player's mind. And lets not forget that the majority of the races that are left are in Earth orbit. If you chose to destroy the reapers this means there's a good chance those races will all die of starvation unable to get home. How knows if the few survivors left will be able to hang on. You may have just consigned nearly all your allies to death and knocked what's left of humanity back to the stone age. Survival becomes questionable there as well.
5) Deus Ex Machina; For those of you who aren't aware this is a literary fallacy whereby the author invents a device that solves the overwhelming issues the protaganists of the story face. It's considered a cheap way to sidestep the issues. Remember SF is an exploration of how advanced tech changes the human condition. But if you simply create a machine to solve the problem the protaganists have no chance to grow or adapt. You short circuit the climax of the story. In the case of a game there's no feeling of accomplishment for the player.
6) The metagame heartbreak; All through the series boiware was claiming that your choices throughout the entire three games would have an effect on the ending, yet everyone got the same three choices with zero variation. Need I say more?
And I know I'm forgetting some of the issues. I'm sure others in this thread brought them up
Now considering the quality of the game leading up to the final mission versus the quality of the final mission it seems pretty clear that the issue was not the underlying story, but deadlines. Based on a few things I picked up in the game I think the original plan was for shepard to find out that the crucible was actually a plant in the prothean database by the reapers as another level of control. The Reapers' goal being of course to get the various races of the universe wasting astronomical sums of resources (not to mention time) on something that wouldn't work. And then when the allies did finally attack their battle plan would be centered around something that would fail. How many ships were wasted protecting the useless crucible? This would have been a master stroke, turning what appeared to be a Deus Ex Machina into a weapon of the enemy and teaching the protaganist something about trusting what they didn't understand. It also fell well within the Reapers' tactics; they left the ME relays to guide the various races of the galaxy along specific technological paths. (BTW this tactic suggests that there is some EM related tech that could be a threat to them). Shepard would call retreat and formulate a new battle plan centered around exploiting the weakness in the reapers' defenses we learned about on Ranoch. This even explained why the necessary forces tracker's minimum force requirement was so low. You'd lose alot of forces in your first abortive assault.
But if none of that bothered you, well at least you didn't feel cheated out of your money.