Do NOT look to Junction. It's just a horrible mess more than it is any particular theme.
The first place you should be looking is the original launch maps (2fort and Hydro in particular, Well a little too) as they have some of the best spytech Valve has made, though I feel all their maps since then have been lacking.
For custom maps the first things that come to mind that would be good to look at are Vector and HAARP.
Seconding Vector and HAARP for customs to look to. (Glad I'm not the only one who writes that in all caps by the way.) I'm not sure why you're hating on Junction for this though. For sure it's a sterling example of how not to make a map, but artwise I don't recall anything too out of place other than the random farm boxes and pallets in the middle of some of the floors.
I recall someone saying that spytech involved irregular angles that nonetheless complemented each other, whatever that means. Was it Icarus? Can't remember...