Alright, let me answer this a bit more concisely. I don't care.

That's all there is to it. I. Don't. Care. A movie could have all the internal logic in the world and it wouldn't make a difference to me if it wasn't entertaining to watch. Nitpicking flaws in the story doesn't make me happy, and it's not why I watch movies. If a story genuinely has flaws that break it completely, then yeah, I'll point that out. But if the movie is fine EXCEPT that there's a better way it could have done something, well, that's a bullshit approach to criticism. Take a movie on its own terms.

I know I diverge from 99% of the people on this forum on this issue, and I'm comfortable with that. Just thought I should make it clear where I'm coming from in these discussions.

Does that mean you're lumping this one in with most Michael Bay movies or are they on a completely different level of suck to you?

Logic consistency, AKA making sense, isn't a nitpicking area. If you can't see why a character is doing something, or why they are doing something in a particular way, then that breaks immersion and is also reflective of bad storytelling - equivalent to someone having to interrupt the campfire story to clarify something. Without coherence in story and setting, then it's just keys dangling in front of your eyes making noises and catching the light. These are the same sorts of problems that face Prometheus and countless other big blockbusters, from Battleship to Star Trek to Man of Steel. Laziness is laziness, regardless of how good it looks.

The problem here is that the lack of thought out into the world building influences the choreography, and the choreography does not match the serious tone of the movie, i.e. mankind is fighting for its very survival. If we had a kung fu movie where the final duel between hero and the villain that murdered his parents lacked the intensity and emotion we would expect, or a lightsabre fight just went on and on, we would lose interest.  Fights between giant robots and monsters actually become boring. I find this to be a problem when it's the main attraction. I point out issues stem in the story because I see their effects on the battles to be detrimental.

I so wanted to love this one, I'm a huge fan of mech anime. But I'm not really entertained watching a man punch a zombie over and over (in a serious movie about the apocalypse). 

To be clear, I really have no problem seeing that people have found it enjoyable, parts of it had me squealing in delight! But let's not claim that it's a good story and features great worldbuilding, or that it's fine except for a few nitpicks. That's delusion.

Also, nitpicking is pointing out that the kaiju couldn't possibly have flown that high on its wings and that Gypsy wouldn't have been going fast enough to experience re-entry burn up, or that creatures that size couldn't possibly exist in the first place.

I only had two minor problems with it...

1. I couldn't see the kaiju and jaeger fighting because it was (a) too dark (b) too wet (c) edited too fast (d) camera too unstable and (e) zoomed in too close
2. Even if you could see the fisticuffs, the fight sequences were too short, resulting in the rest of the movie playing like a glossy Asylum straight-to-video job with D-list actors and 10 clichés-per-minute screenplay.

I wanted giant monsters versus kickass robots in a Matrix Burly-Brawl punch-up trashing Manhattan.