I only just now finished the game. When the game just game out I was still finishing another title and with all the talk about the bad ending I sort of let Mass Effect 3 slide for a while. Despite it probably being my favorite series this generation. And in hindsight that was a dumb thing to do. I can honestly say I really enjoyed part 3. I do think it has some flaws, but nothing that kept me from thinking this was one of the most enjoyable games I have played in a long time.
I mostly was disappointed the side missions where just picked up by passing conversations with generally just a scanning mini game attached to it (which was less fun then the scanning in 2). I would have preferred to really talk to these people and done some real side-missions for them. some did involve talking yourself and I got all excited for example when the Elcor asked me to help with their homeworld being under attack. Only to find out it was a scanning mission. I literally dropped everything else I was doing to go and help these gentle giants...
Other minor nitpicks where the simplified currency system and dialog trees. But I did like how you had to find upgrades around the missions. I just never really got into the entire, upgrade your gun thing. In that sense I am glad they simplified things since ME1.
I actually did not really have a problem with the ending. It's not great, but all in all.. it was an ending. I was a bit disappointed with the options I had as none of them where what I wanted. Plus it's odd cut scene at the end about the people who fought directly at your side. But I didn't hate it. I kind of saw it coming. It was hinted at before through ME3 (I think the reaper you fight who controls the Geth kinda mentions it) and in ME2 as well. But hey I also liked the ending of Enslaved and everybody seems to hate that one too.
Spoiler in regards to the end:
What I found daft about the options is that: the synthesis didn't run with me because I felt I would force this choice upon all living beings without them wanting it and the destroy option would kill the Geth and EDI. While I was proving that synthetic and organic could co exist. So I picked control as in that case everybody could live, except for shepard. Main gripe might be however is that I loved the universe setting and the ending definitely changes that. I would have loved a post reaper invasion game where the universe you've come to known and love is still there. Be in war-torn... Now that's pretty much not an option anymore. But I did have a good sense of closure.