Setup can make a mess of a course, obviously, but there's no need to talk about that.
Setup can also make a course much more boring and repetitive than it should be. That could be the fault of the superintendent or assistant in charge of the setup, but nowadays it's more likely to be the fault of his bosses insisting that the course be set up consistently so that it's within the bounds of the USGA Slope System.
For example, if you have three par-3's that are all around 200 yards from the back, you could alternate and play one of them at 200 and one at 180 and one at 160, so you play all three at all three yardages over three days. But that's way harder to do if your club has rated four different sets of tees and they want you to keep all four markers within a few yards of the plates, which is what the USGA says you're supposed to do so all their fancy numbers don't go out the window.
And, though you may not be speaking of green speed as a part of setup, giving the superintendent a speed which he's supposed to keep every day of the year severely limits the flexibility of setup and using marginal hole locations that you could otherwise use on slower days in the spring or the heat of the summer. But, some superintendents INSIST on having a set speed to keep, so that they have a concrete standard and nobody can complain to them if they're meeting it.