The ME3 ending, in a nutshell, invalidated every single choice that the player had made over the last 3 games. Every single choice you made meant nothing, the ending turned into a binary "here's three endings, choose which one you want by pressing this button". Choice, which was something that lauded in the ME series, played no part in 3. They hyped up this galactic asset crap, where you would bring together as many war assets as you could so that you would have a better chance of fighting the reapers. There is no difference between getting every asset and getting none, because the endings are completely independent of it and just flat out ignore it.
It also betrayed the overarching themes of the games. Throughout the Mass Effect games, Sheppard has always been told that "it's impossible, you can't do it!" and in every game he's said "fudge the odds!" and overcame the impossible. At the end of 3, some space magic god child tells him "you're fucked, here's your 3 choices" and Sheppard sits there and takes it. For a story about one man overcoming everything, he gives up incredibly easy and no matter what you choose, dooms the galaxy to a dark age.
There's absolutely no closure. Throughout the three games, you develop these relationships with these characters. You become friends with some, you fall in love with some, but you learn nothing of what happens to them after the end. They end up crash landing on a planet with no way out and... that's it. I want to know what happens to these characters that I have spent the last 4 years and 4 months with. And what happens to the rest of the galaxy with the entire combined fleet stuck in the Sol System with no Mass Relay to let them escape?
Not to mention the myriad of plot holes and inconsistencies.
also, space magic.