This seems to be one of those problems where it's difficult to decide if Skaven are too good, or if the other armies simply need to be better optimized. Other people have outlined (much better than I could have) the fundamental problem with Skaven: everything works well together, and it's all cheap.
A friend of mine doesn't even play the fully optimized list (no WLC, HPA or screaming bell) but he does play with a horde of plague monks pushing a furnace, multiple plague claw catapults and several slave buses, even this "sub-optimal" list is fearsome. I don't know if Skaven stray into overpowered territory, but I think their army fuses together much better than other armies, and I think future army book authors should take note of the Skaven book, and try to emulate how well the units work together. Perhaps synergy + increased unit costs would make Skaven more bearable, but right now I'm feeling like they're at best overtuned, at worst OP.