Can't wait to hear Michael Bay's comments about the VFX upset. I mean, you know he will have something to say.
Golden Compass over fighting robots? Get the fuck out of here, seriously.
I never in my wildest imagination thought about real life giant robots fighting on screen in warzones, fucked up designs be damned. It looked amazing and was truly a feat combining a LOT of real footage blended in seamlessly with GIANT FUCKING ROBOTS!
But yeah, Golden Compass 
Transformers looked like ass. I've said this from day 1. Whether they were technically more proficient or not is beside the point when the effects look unpleasing. The terrible faux-organic-inspired design made the robots look like messes when they were grappling together on the screen. As I've said before, it was difficult to tell where one robot ended and another began in that final sequence. I think there's only one truly impressive sequence in the movie (the desert fight with the military peeps. Not the opening one; the one after).
Transformers does nothing well. It might actually be Bay's worst movie.
Unfortunately, most of what you write is true. It took me several viewings before I could recognize the subtlety and nuances in the designs. They were bad, but there were details to be had. It was just confusing with the fast cuts and different shots during the fights, it shouldn't take several viewings to understand what you just saw.
That said, the amount of planning and destruction that took place in real life, combined with there looking like there are giant real life mech's fighting and flying around deserves merit and recognition.
I think it's unlike any other special effects movie I've ever seen in that regard. It got robbed by cgi polar bears.
BUT, it's not a travesty on the lines of say, Children of Men not even being nominated for Best Picture. In the overall scheme of things Transformers was a small snub. I just think it was a lot more of a technical marvel than it's given credit for, and I haven't even seen another Michael Bay movie to be honest.