MASSIVE SPOILERS:
Just take a look around at the general consensus on the internet, and you'll know why I hate the ending.
Here is one article that looks into it:
http://www.gamefront.com/mass-effect-3-end...fans-are-right/
But, for the sake of discussion, here are some of my top reasons, in no particular order:
1) All three choices are the same. All that changes is the color of light shooting out from the Mass Relays, and whether or not Shepard can live.
2) Lack of discussion with Catalyst AI. Throughout the series, I have built my Shepard to be inquisitive. I've always been able to ask questions. And yet, with this AI, there isn't even the option. It all pretty much just plays out in a cut scene. So, you're telling me that Shepard isn't going to pry the Catalyst for a little knowledge? Ask it what it projects will happen for each option?
3) Bad logic. So, the Reapers exist to wipe out advanced organic life, so that synthetics don't destroy everything. I hate that the Reapers exist for that, I was hoping they'd be so much more intriguing, but whatever, can't change it. Anyway, their determination is completely nonsensical. Why anyone (the most advanced AI in the galaxy, for that matter) would believe their logic astounds me. So, how did this race of long ago determine this? Because what they created was going to wipe them out? So, they conclude:
a) That this will happen to every advanced race

That they will stop this by leaving people the Mass Relays and other technology they created. The same technology that inevitably LED to synthetics destroying organics. Prime example of a self-fulfilling prophecy.
The worst thing about this is you can't even make a case for yourself. I don't care if the Catalyst would have accepted the logic or not, the fact that Shepard can't make a case is idiotic. So, you have a human and AI relationship (Joker and EDI), and the Quarians and the Geth are now all buddy buddy. Hey, look, things won't always end how you think. There are anomalies, things could be different this time. But no, I don't even get to argue it.
Hell, they don't even let you make your case for the meaning of life. The idea of making choices and owning up to them. Instead, Shepard just sits there drooling and makes a choice that he has next to no information on. And who the hell is Shepard to choose whether or not ALL LIFE IN THE GALAXY becomes a mix of synthetic and organic? How exactly does this Mass Relay pulse cause this?
4) The Catalyst Star Child. Minor complaint, but the scene would have been much more effective if it had been a Reaper voice, like Sovereign or Harbinger.
5) No closure. So, the Mass Relays blow up. Remember the last time that happened? 300,000 dead. So, Shepard probably just killed billions of people. But whatever, no need to go into that. No need even see a slight montage of the repercussions your actions will have. We'll just give you some stupid ending the a guy and his kid.
6) Joker and the crew. How did he get everyone? The power of friendship? Why was he doing a Mass Relay jump?
7) Your choices throughout the series do not bear any significance to the ending.
Straight from the Bioware Mass Effect 3 site:
Quote
Experience the beginning, middle, and end of an emotional story unlike any other, where the decisions you make completely shape your experience and outcome.
Bullshit. My choices do not shape the outcome. The only thing that changes is Anderson living or dying and the condition of Earth. But in the end, I don't care about that. Those things really don't matter. A single character living, and the survival of a planet that, until this game, had zero significance to me?
I'll stop there for now. I could rant for hours.
It's really such a shame. The ending scene with Shepard on the citadel, bruised and bloody and torn apart, with the battle for Earth going on right outside is amazingly well done. The music is stellar. The entire moment is just ruined by poor writing. I'm not upset that things were rather tragic - hell, I read that originally Garrus and Liara were supposed to be killed by Harbinger at the end, but Shepard has to continue on without even a backward glance because completing his mission is paramount. Heart wrenching stuff.
I'm frustrated that it doesn't make sense. I don't need a golden ending where I ride away in golden armor riding unicorn with Liara. I just want something logical, something that fits with the themes of the series, something that takes into account the choices you made, something that provides at least a small amount of closure. Bioware promised our questions would be answered, but instead they just created more questions.