1. My point is that you are saying people would not have been pissed if Shepard left his crew behind to die. My point is that whether or not something "makes sense" isn't going to prevent people from behind pissed. The Normandy leaving is a perfect example of a scene that makes realistic military sense but was lambasted anyway because people didn't like the endings in general and wanted to find reasons to put down any part of them. I feel like this is the same way, though for the opposite reasons.
2. He leaves because Shepard is knocked out on the ground. Notice when Shepard wakes up he's already leaving. And Shepard doesn't get evac'd because he's fine; his crew was physically unable to conitnue.
3. It's not a plot hole. Unlikely sequence of events isn't a plot hole. It's a plot shield though. 
As for your last point that is fair, I'm not going to tell you how your feelings are wrong. I would actually be interested to know how out of place it felt for people playing it for the FIRST time. It will feel out of place for us no matter what, obviously, knowing how it went down previously.
1. Sorry I was confused. I thought you were talking about in game characters being mad. Well I I guess I just see more people complaining about plot holes but then I certainly pick and choose my threads.
2. Well him leaving also bothers me sorry

I mean this seems important so why would he leave it's pretty unlikely he got everyone. Hedid not only miss Shepard but also Anderson. It just seems so cliche that the villain leaves to celebrate at the end and gets defeated. me usually does better.
3. Well I agree that sometimes you can suspend disbelief for a good dramatic scene. Still e mark of good story telling is plausibility and this seems a bit too far out there for me. T plot holes are never impossible to explain you can always make up something, look at IT

I actually laughed the first time on this scene, I guess the moment wasn't quite there for me but I agree that most people probably did not think somuch about it the first time.