The show powers through logistical implausibilities time and again, which has been true since the first episode, really. But that's not the same thing as being a nonsensical mess. The smallest details are incredibly well thought-out, particularly in Season 3-5 (though the attention to detail in 1-2 is nothing to sneeze at either). The show rewards multiple viewings, rewards thinking about at length, studying carefully. But this isn't realism we're dealing with. I think getting too hung up on how realistic certain things are -- though I fully confess I'm frequently guilty of it it myself -- is kind of a waste. The implausibilities of Breaking Bad are certainly no worse than any Western you could point to, and that's what the creator thought of the story as. There are plenty of terrific Westerns, but anticlimactic realism isn't exactly what that genre trades in.
What's important is that the show is consistent to itself, and the characters are consistent to themselves. The themes are consistent to themselves. And I don't think they ever fully dropped the ball on any of those things. There are a few bits here or there that I question a little, in terms of characters' decisions or actions, but there's nothing that I just flat-out don't buy or that jars me out of the show's spell. I wasn't too thrilled with Jesse's doofish confusion about a bystander being a hitman Walt hired; and Uncle Jack plays into Walt's final gambit a little too easily, probably. But these things are so minor compared to the sins of most serialized TV shows, and counterbalanced by such dazzling high points.
I don't find it to be a very cloying show, emotion-wise. It gives wide berth to a lot of sentimental gimmicks, when compared against the rest of the medium. That's not to say it doesn't manipulate viewer emotions, but, I mean, come on -- that's simply a part of storytelling. I vaguely remember you (I think it was you) had high praise for the movie Source Code, which threw its whole set-up away to end on a cheesy Kodak moment, as I recall. Gilligan & Co. manipulated audience emotion with intelligent precision, interesting aims, and an appreciation/respect for the audience's own intelligence. Making you feel good just for the sake of making you feel good isn't something I think very many people would accuse Breaking Bad of.
If we're just nitpicking logistics though, of your bullet points: #1 didn't bother me (Gretchen deactivated the main house security, and I accept that Walt is smart enough to get as far as their courtyard without having to be walked through his whole process). #2 -- I like the AV Club write-up's attention to the finale's focus on machinery that keeps moving on its own, and tying that to the predictability of certain characters. Walt is a chemist and by the finale, people are just another ingredient. He knows how to use them now, mix them, predict them, almost as skillfully as chemicals in a lab. This is illustrated early in the episode with the phone call he places to get Elliot/Gretchen's address. But anyway, yes, Lydia's fastidious, schedule-oriented nature was embraced as a fundamental part of who she is, a part that could be reasonably counted on, and exploited. #3 -- I liked the shot you're talking about, but I do get a kick out of your description, made me laugh. #4 -- I agree with this. #5 -- if anything, I thought it more strange that he got hit at all, especially with any degree of lethality. He was safely below the horizon-line of fire. #6 -- I didn't find the dramatic payoff to be trite, but yes, it all works out a little bit pat.