1) So writers are gods with unlimited intellect and can't make mistakes. Did you ever heard term plothole? This is than writer forgets/make mistake pothole happens. Or Akira Toriyama writer of Dragon ball Z manga forget character Launch. It's not good writing if majority of you audience instead of enjoying ending or crying how sad and touching it is, go wtf happening right now. Or you telling bioware released free DLC to explain why we all stupid and don't understand great ending just because they nice. ME3 ending are nonsense and unsatisfactory so big even EA did something it wasn't good think but they still did it. It was middle finger you don't like our great ending you want to refuse starkid nonsense "SO BE IT" you lost and you die, well at least this ending make sense.
2) I agree it fits on some level. Even if I just made peace between Geth and Quarian and can't tell to catalyst "I just solve you problem you moron even with you trying to sabotage it.". It was just represented horribly, but still theme could work if ending fixed a lot.
3)I never think reapers are bad. It same as pig I eat think I am evil monster. I always think since Sovereign speech that reapers think we can't comprehend is reproduction. They "eat" us and make more reapers like any living organism. I never could imagine they "saving us".
Sorry to just jump in, but...
1) I want to know what the plot holes are you're talking about, and also what the EC did that made the original ending "better". They haven't changed any fundamental plot points in the story, they only expanded on it, and quite frankly, what was added could've been thought of by people themselves had they tried.
2) This peace between the geth and the quarians is not exactly a good example imo. You know why the "peace" happens? Because you hold the fleet back by telling the quarians they will be annihilated if they wouldn't. If you let Legion continue to upload the Reaper Code, it would tear the fleet to pieces. So with their backs against the wall the quarians let you blackmail them into stepping back. It's either death or survival. Of course they step back to guarantee their survival. And if you can't broker peace you are the factor that decides over the fate of the geth and the quarians in a similar way, so this is settled via outside source in both cases. I'm sure without Shepard's intervention the geth would've wiped out the quarians. Doesn't matter in this case who started which war. The organics would have been killed by the synthetics, just as the Catalyst has observed who knows how many times.
3) That's the problem that you can't imagine them saving us, and exactly why the Reapers say that organics cannot comprehend. I would advise you to read the Retribution book, Karpyshyn touches on this topic.
Also anyone who still doesn't see the organics vs. synthetics thing... think about who we fight, what they are. Imo ME2's mistake was to focus on the loyalty missions and not on the plot that could've pushed the theme even more into light. Yet it was still there as our main theme the whole time.
Hell, even Drew Karpyshyn spoke about this theme in his blog and I bet many people think Mac and Casey made this theme up the last minute. Sorry, but that's not the case.
This is like if you take stuff that's presented to you in a history lesson and you deny it because "Oh, I wasn't there. I'm sure these guys are lying and this is not what happened because XYZ". If the Catalyst says this is what happened in the far away past, sure, it could be lying, but who are we to judge it? We haven't been there. It can be true after all. But people here don't even want to consider this, because... hey, we didn't see it in this cycle (which is untrue, but oh well) so that thing must be lying and it's non-sensical.
If they were open that this conflict might be a thing and that's why everything happens how it does, how the cycles came to be... then I'm sure we wouldn't have so many raging fans.