I think that Desert and Spytech are somewhat justified in their appearance in so many maps simply because they're pretty much the core of TF2's overall "theme." A whole 4 of the 6 original maps (2fort, Dustbowl, Gravel Pit, Hydro) were some direct variation on the desert theme, and all 6 had Spytech of some form or another (Gravel Pit was minor, but still the RED spawn was Spytech-esque; all the others had blatant spy bases). Many of the official maps that followed, and several community ones, were also desert because that was the primary, defining theme of TF2 for a while. While it can get tiresome, it's the basic foundation of TF2 itself. So both themes get some forgiveness in my mind for their near-omnipresence.
Personally I vote for Alpine as most overused because it seems to be very hard to get right, and many, many maps exist that use it and don't seem to get it right, resulting in a dull and uninteresting environment.