I liked the ending in a sense. Before you shoot me and call me an indoctrinated agent of Bioware, let me explain.
The ending made sense. The Citadel has been key since the beginning, it's always been there - The Protheans discovered it and used it, as did the Asari/Turians/etc/Council. It's revealed in ME:1 that it's actually a Mass Relay and that it was built by the Reapers (or so the Prothean VI thought).
In reality, the Citadel houses the VI responsible for controlling the Reapers. One thing I wish Bioware would have explained is the connection to Harbinger (the most powerful Reaper is hardly ever mentioned in the story

) but nonetheless, Shepherd finds this VI and then you begin the fun discussion of - "To kill, or not to kill, that is the question."
If you choose to destroy the Reapers, all synthetic life is destroyed (including Reapers, Edi, Geth, etc) as well as the Mass Relays and the Citadel itself (wiping you out along with it). If you don't have Galactic Readiness to 90%+ or whatever, most of the fleets are decimated in the final attack so almost everyone dies.
Is it a good way to end the series? Sure. You destroy the cycle of destruction that you discovered at the end of ME:1, you save humanity (your #1 priority) and give your life in the cause (Shepherds purpose). But, as Bioware loves to point out, everything has consequences - the penalty of destroying this cycle is losing the technology the Reapers created, namely the Mass Relays. Thus humanity is now forever separated from the Reaper threat/technology, but also from further Galactic Exploration.
Are there loose ends? YES. THAT's what bugged me the most. I had at least 20 different questions AFTER I beat the game. The game's ending SHOULD have answered all of them.
Questions such as -
- The Reaper VI - who created the VI? How has it survived for so long? Why did it take the form of the boy?
- The vision of Shepherd and his "son" - what the hell is this here for? If you're going to die doing the right thing, then it's not going to happen, so is it just some pointless "if the Reapers didn't exist and you never did any of the stuff you did, you could be doing this" thing?
- What exactly just happened?
- What happened to the fleets in orbit around Earth? How are they going to get back to their respective home planets without the Mass Relays?
- What exactly was the Illusive Man? How exactly was he tied to the Reapers?
- What happened to the rest of your crew?
- Is it possible to rebuild the Mass Relays?
- The future of the Protheans. If you do the From Ashes DLC, you get a (spoiler) a Prothean on your team. If he survives, he's the last member of his race, one of the most prominent races to have ever existed. C'mon, go somewhere with this!
- What exactly did the Crucible do? We see an image of the beam washing over Earth and people getting vaporized, well what the hell? Did it just destroy humanity anyways? What exactly did it blow up?
- Etc, and etc.
I think the ending was good, but not enough. I had to do a lot of reading online to sort of close some questions but even then, I'd love for some more answers. The basic structure of the ending was correct when you think of the ME series as an Epic, Shepherd as the Hero and the Galaxy as the people.
The Hero must save the people by sacrificing himself to stop the unbeatable power.
It's a pretty common story-ending, and it's been in ME since the beginning. Bioware followed up with it, but they should have worked through all the holes it left.
Those are just my thoughts. Bioware's mentioned that they won't make an ME:4 (Shepherd's series is done) but that they might make more games with the Mass Effect world (I, for one, would love to get an RTS game for ME based off of the game Star Wars: Empire At War. That would be incredible). They might go into more detail in those.