I feel like there is a kind of "uncanny valley" mentality here. "uncanny valley" being the phenomenon where a live person is comfortable with a cartoon representation of a human, but then gets really uncomfortable at the area just before the representation achieves full human likeness. The "almost human" appearance somehow makes it even more apparent that something is wrong with it.
http://en.wikipedia.org/wiki/Uncanny_valley
A similar attitude seems to be going on here where it seems that a more complex simulation engine has made certain flaws in it to be a lot more significant in perception. SimCity 1 through 4 was basically an Excel spreadsheet with building graphics pasted onto it. No one gave a shit, though, because they were great games. I don't think many people really gave too much deep thought at what was going on "under the hood" so to speak, and, just like a cartoon representation of a human, people's minds just filled in the blanks.
With the new simulation engine of Glassbox, I think the inherent expectation of a really complicated simulation engine makes flaws in the system that much more obvious and distasteful. The closer and closer we get to a more realistic simulation, the more obvious that performance shortcuts and programming deficiencies stick out like sore thumbs.
In the end, SC5's simulation engine is more complex than the other games, and it can only improve from here on out. I'm just saddened that the EA PR doublespeak, stupid design decisions, and terrible launch preparations, among myriad other things, ruins what is otherwise a pretty decent first iteration of a reboot. Still, these recent paid betas are fucking ridiculous.
But maybe it's just me. After all, I did play Final Fantasy 14 and Diablo 3 for a while, too. XCOM didn't give me any problems, though. <3 Firaxis.