There is just a kind of emptyness whenever I think about the ending. I've never really gotten angry about it, but then it doesn't evoke anything strong at all in me. (I can contrast this to curing the genophage in ME3, the ending of ME2 and the mission on Virmire in ME1 about which I have clear thougths and feelings)
The ending was originally just kind of confusing for me. I think the problem is that the tone suddenly shifted miles apart from the rest of the games. I don't mind some abstract questions but they didn't really fit here. Yes, there was some organic vs synthetic themes in the rest of the games but that always felt like merely one theme amongst many. The synthetics (the Geth, EDI, that one AI from ME1) were another 'Other' so to speak, along with quarians, humans, krogan and everyone in the story from somebodies' perspective. More importantly, there is no reason why sythethics and organics have to be at eachothers throats any more than organics are at the throats of other organics already. A lot of the story of mass effect was about living happily together, tolerance and all that hippy shit. That is why Joker and EDI end up together and why the Quarians and the Geth can both survive the storyline and that is why humanity, despite the first contact war and the general mistrust everyone feels against them can get reasonably along with the rest. It is why the good ending where you end up with a lot of paragon points to the krogan storyline is the one where you cure the genophage. After all that, SC's assertion that synthetics and organics can't live together just fell flat for me. If you want to give the enemy of the entire storyline a motivation it better make sense on some basic level. None of this should impress shepard in the least.
At the time I didn't really feel anything strongly about it. I thought, 'yeah, I see the themes they were going for but it didn't really work, I think.' None of the specifics make any sense though. There is a line were SC says 'the fact that you stand here proves we cannot continue harvesting civilizations.' This is just not true. Shepard is weak and barely understands where he is anymore. A single collector footsoldier flying in with a gun could kill him and the reapers can continue their cycles. There is no reason to fire the crucible yet SC allows shepard to do it.
The most damning thing I can say about the ending though is that whenever I think about any specific part of the canon, even reaperrelated things, the ending just somehow doesn't feel like it counts or like it can give me meaningful information. Something about it is just so entirely off, that it feels like it never happened to me. (not within it's own universe, I mean) Everything inside the citadel with TIM and SC feels like it isn't properly part of the story and merely a tacked on fable. A fable about organics and synthetics which perhaps sheds some light on something but which just isn't an ending to the story I was playing through.
There is a long video by mrbtongue on youtube about it where he says that the story loses it's cohesion. That, I think summarises what I have been saying in this post quite well. I don't really think or feel that much about the ending because I can't really see it as an ending to the story I cared about to begin with.