I honestly never got the big deal about the ME 3 ending. Ok, so the last 15 minutes of a game I got 28 hours of enjoyment from weren't great. So what is that? .8 % of my time spent playing the game was unenjoyable. It's UNDENIABLY the best of the bunch mechanically, Improved on mechanics introduced in ME 2 (which were the reason ME 2 was a substantially better shooter than ME 1 was) while bringing back some of "baby with the bathwater" mechanics that were tossed in the transition from 1 - 2 like weapon mods. The story right up to the end was also very well done. The Mordin story line in particular was wrapped up extremely well, but basically all of the party member missions were spectacular as they were in 2. ME 3 had SO MUCH going for it that what on the whole was a very small portion of it going horribly wrong just wasn't that big a deal to me.
Granted, the ending was a small part of the game, but it was THE most important one. So yeah, it mattered.
For a couple of reasons :
1) Bioware promised that ME3 would have a dozen endings depending on decisions made in all 3 games combined
End result : 3 endings that only vary in 3 different color of explosion. So they lied basicly.
2) Closure : Every good story needs one. And ME3 had none (the original ending that is). What happened to earth? WHat about the other races stuck in our solar system? Plot holes everywhere
3) No choices : Option 1 : DIE / Option 2 : DIE / Option 3 : DIE. DA:O's ending gave you many choices, you could sacrifice yourself, but you could also let an other greywarden do it. No such options in ME3. Some people don't want a sad ending.
4)The ending was so vague that some people started to invent an different ending (AkA, Shepard was under indoctrination all this time). This gets us back to the lack of closure the ending had.
I'll give credit to BW for actually trying to set things straight with the free patch that ironed out the ending.
You're right, the ending alone is not enough to make it a bad game, but the disappointment is justified.
The problem people have with the controls is kinda similar. The game is actually good, but the controls leave us with a bad impression.