I played to the end of Mass Effect 3 last night, mostly to understand what all the hubub was about. A friend of mine was raving about how it made no sense, about how it was "total garbage," etc. I thought it was fine. I liked it. It turned out pretty much exactly how I knew it was going to. There are a few plotholes, but nowhere near as many as most people are complaining about.
Note that from here on in are some enormous spoilers.
The "twist" at the end (if you can call it that; everything in the game pointed to it) was hardly unexpected. So the Reapers built the Citadel and the Mass Relays. I think we were told that in ME2 if we followed a certain dialogue sequence with someone or another. The Crucible is more or less reverse-engineered Reaper tech, turning the Relays against them. Okay.
Most of the "plotholes" can either be explained or chalked up to "video game magic". Don't tell me Mass Effect can't have video game magic, because that's exactly how the titular "Mass Effect" works. Even if you somehow decrease the mass of an object until it has negative mass, the speed of light remains the same. Eezo doesn't change the laws of physics.
For example, my friend asked me, when I told him it all made sense, how did Joker get all the team away from Earth in time to avoid the explosion? Video game magic. How did I have time to talk leisurely with my entire team before firing off missiles into the Reaper guarding the beam up to the Citadel? Video game magic. How do I always seem to stumble upon Cerberus attacks at just the right time, even if I spent what must equate to several in-game days flying all over doing other things? Video game magic. It's part of the suspension of disbelief required to enjoy these games.
There's the big issue of everyone rebuilding, of all the fleets stuck on war-ravaged Earth and not having enough food. If you brought the Quarians along, they're not even carbon-based life forms so they can't eat Earth food. The answer is that yes, some people will starve, and yes, the Quarians will have a tough time of it. But the Quarians have been growing their own food on ships out in space for centuries. They'll be okay. And Earth may be a bit scorched, but the Reapers weren't exactly destroying farmland to try to starve us humans to death. I'm sure that most of the underpopulated agricultural land on Earth is still just fine.
When Shepard got blasted by the laser, I thought he was dead. It seemed to tear everyone else to bits, after all. Whether or not he actually gets up afterwards is open to interpretation, but I think he did. This is made a little funny by the fact that he's wearing his N7 armour even if you're wearing something else before. I can't decide if this is an intentional plot device to suggest a dream, or just lazy modelling. Judging by how Shepard's helmet seems to pop on and off without much rhyme or reason throughout the game, I'm leaning towards lazy modelling.
The whole indoctrination "theory" floating around the webs isn't a theory, it's what you're meant to assume happened. Maybe Bioware didn't make the cues loud enough, but it seemed pretty clear to me. Sure, the details on when and where are a little fuzzy, as well as exactly how much of the final scene is truly real, but the plot itself is solidly planted for all to see.
The one thing I can say is a big plothole is the destruction of the Mass Effect Relays. It was mentioned earlier that blowing one up tends to destroy the entire solar system it orbits. I know that Bioware can easily just say "Oh, the Crucible destroys the Relays from the inside out instead of with conventional firearms, limiting the blast" or something like that, but as it stands, it reminds me a little of the destruction of the Death Star in Episode VI and how it should have destroyed the moon of Endor (they did clear that one up; Star Wars canon now states that hours after the party scene at the end of the film, all the humans leave and the shockwave from the Death Star arrives and vaporizes all the Ewoks. They were so cute, too).
On a whole, though, I don't understand why everyone's so upset. I suppose some people expected more distinct, separate endings, but the story of the trilogy is a bit too weighty to really be strongly affected by whether or not you shot Wrex in the first game. Get over yourself.