1.)Possibly the most major reason - it's ridiculously brief. Bioware has built a really rich universe, other games take about 50 hours to complete with DLC included - you've made tons of choices through those games that Bioware has repeatedly said will matter.
And then they didn't deliver. Instead you're given an ending that lasts about 10 minutes if you include the entire part starting from the laser. Even that's hard to include as no matter what you do during that sequence (which is pretty much Shep limping through a railway) the final choice comes down to 3 options. All of which end in VERY similar cinematics that gives no epilogue or followup - all you know is what happened to shep.
2.) What the fuck is happening factor. The end of the game seems like an afterthought in which very little makes sense or is developed. Not only do they introduce new characters, they introduce entirely new concepts in the last minute of the game. Not only that but there are plot holes all over and they're absolutely crazy:
How did Anderson - who not only charged the conduit AFTER you, but is also significantly older than you - reach the control room faster? Where in the fuck did the Illusive man come from? He just walks in with no explanation. What in the actual fuck is the catalyst? An AI? A VI? Harbinger? God? He simply says "he" came up with the whole system as "his" solution. Why does he take the form of the child? Was the child real? etc. And not only that, what kind of solution is: "Hey you guys are eventually going to make synthetics that can kill all of you organics. So instead, I made some super advanced synthetics to kill you all so that you wouldn't make synthetics to kill you all. What?
3.) There is no epilogue, and the game REALLY DESPERATELY needs one. In every ending, you destroy all the mass relays. In the arrival, it's revealed that the destruction of a mass relay results in an ENTIRE SYSTEM being destroyed. So not only did you completely fuck everyone no matter what you picked (presumably) even if you didn't you fucked space travel forever, and I doubt all those ships have the supplies to get somewhere without the relays. So you screwed everyone over anyway? Because if you didn't, you should be told that you didn't.
What the fuck, normandy? Did all my allies just flee the fight for Earth? All those guys that all were saying they had wanted to STAY at earth the entire game... They just abandoned the final fight? I'm supposed to believe that?
4.) What happened to all the themes the ME series was building up to an ending for? Free will/the meaning of life? Synthetics vs organics? Unity? Where the hell did all of that go? You're pretty much told - unity can never happen, you're retarded, go kill yourself Shepard. I just spent an entire game and ended up getting EVERY RACE INCLUDING THE GETH to unite for a common cause. And I'm told that that can never happen. What.
So yeah, the complaints are pretty valid.