Like a lot of the posts I've seen here, the only really bad part seems to be the endings, which were overwhelmingly depressing and made me feel like the majority of the game was spent preparing for war, only to have it wasted.
I got the Turians and Krogan to work together, managed to wrangle the Asari and Salarians on my side, not to mention assets from the Batarians, Hanar, Elcor, Volus, and Drell, the Terminus Forces are on my side and I didn't have to do too much that was stepping out of my Paragon leanings. Then I prepared the Citadel for attack, and got the Quarians and Geth to get along. Even with the 'Good' Ending where you can destroy all synthetics, EDI and the Geth are screwed. Synthesis seemed too vague for me, and I wasn't willing to stoop so low as to control the Reapers.
Personally, I am only a little upset that Shepard ends up dead no matter what, but galactic change on that scale? How can they make any more Mass Effect games that feel like Mass Effect still? Either the Geth are gone entirely, the Reapers are around still and possibly even messing around with everything, or everyone is fused to some sort of machine. That, along with the loss of all the Mass Relays and the Citadel? I'd love to see how Bioware reconciles this.
Don't get me wrong, I love the ending, but I would definitely have preferred an ending similar to Mass Effect 2's, only more intense and grander in scale. This... Just makes me sad, disappointed, and feel like Shepard went through all of that for nothing.
[EDIT]: After having started my Fem-Shep play-through, I think I realized the key to why the endings were so dissatisfying: They don't feel like they belong in Mass Effect. That, along with the dreams with the kid in the forest felt out-of-place.