Well, here's a quick list of things I disliked in ME3 other than the ending:
1) Cheap forced drama and attempts at amplifying it with sad piano music. Example - Grunt's Disney Death scene.
2) No neutral dialogue options. Seriously, WTF?
3) The fact that Diana Allers even appeared in the game.
4) Too much arcade stuff - arrows that appear when you are about to leave cover, stupid combat rolls and CoD-like little X marker every time you hit a target.
5) The beginning. Keeping Shepard locked up for 6 months and not doing anything about the imminent Reaper invasion just makes everyone in the Galaxy look like idiots. It also ties with...
6) ...overpowering the Reapers and...
7) ...making the war look like a lost cause from the beginning, with all planets and colonies getting annihilated and so on. It would have been cool, sensible and easy to use the preestablished lore and elements from the story so far to create feasible and dramatic solution to make the Reaper War incredibly hard and dramatic, but winnable in the end. I could really keep right on going on points 5, 6 and 7, but in the interest of keeping it brief...
8) Turning Renegade actions from action movie gold to sadistic evil psycho stuff.
9) Thane's death. Not that it happened, THE WAY it happened. Which brings about...
10) ...Kai Leng.
11) Cerberus Evil Sith Empire on Rocket Boots.
12) EDI's body.
13) Javik. Seriously, I hated him. I bought From Ashes without knowing what it was, there were rumours of a Prothean squadmate but I thought they were a joke, and then... Blaargh.
14) Multiplayer having effect on the story.
15) GODAWFUL weapon upgrade system. Seriously, I hated it. These 21st century silencers and optics look horrible on ME weapons. And they are 21st century optics, with one optic sight they just used a shape of a real life combat sight called ACOG and put it on a pistol... backwards.
16) The vent kid playing with Normandy model at the beginning, the vent kid in a vent, then dreams about vent kid. Although that falls into "forced drama" category.
So here you go, just of the top of my head. Not in order, not sorted from worst to least worst, just what I remembered now. And none of these were in previous games, except maybe for streamlining the dialogue at times in ME2. So yeah, there's a lot to dislike about ME3.