There are (at least) two ways of understanding evolution and making predictions about the kinds of things that it produces. The first focuses on the organism, and says things like, "we expect evolution to produce organisms that are good at reproducing." This is the high school biology level of understanding natural selection. The second focuses on the gene, and says things like, "we expect evolution to produce genes that are good at replicating." This is closer to reality and further from (y)our intuitions.
I highly recommend The Selfish Gene for an explanation of the gene-centered view of evolution. This book cleared up much of my own confusion, and answered a bunch of questions that I had, coming from an organism-centric perspective. Questions like these:
It's also an enjoyable read and full of citations and experimental results.
If you aren't familiar with case studies like sickle-cell anemia, lactase persistence in humans, sexual selection in peafowl plumage, etc., you should probably read a good textbook on evolution before doing any more speculating.
"Pulling some hormonal levers" is highly non-trivial. Think about what sort of genotypic change is needed to affect the relevant hormones at the right age, in the right tissue, without side-effects. Read up on Accutane (isotretinoin) to get an idea of what else can happen when you try to get rid of "zits".
Also, what gives you the idea that we are anywhere close to any sort of genotypic equilibrium?
Not every trait necessarily confers a specific evolutionary advantage. Some traits may exist as side effects of other traits that do confer an advantage, or they simply may not confer enough of a disadvantage to have been bred out of the population.
Severe acne can run in families, but in general, zits are the result of pores being blocked so that the oils released by sebaceous glands build up. I doubt there is a specific gene or set of genes that causes all pimple formation. One's susceptibility is probably increased by genes that influence one of the factors in the formation of zits, if the heritability is genetic in origin. In general, though, they seem to be just a relatively minor (although irritating) malfunction of the dermal system.
What the hell is the evolutionary advantage in having zits?
A zit is how a bacteria makes more bacteria.
An important thing to realize is that evolution doesn't actually care or think. For a human, if a small change makes a significant difference in say, car safety, it's relatively easy for other humans to adopt this same change in all cars, and it quickly spreads. Evolution, on the other hand, can only effect gene pools through breeding rates and survival. An acne resistance gene might be all upside, but if people with zits still breed at the same or nearly the same rate as people without then it won't spread at anything like a noticeable rate.
In addition to the other points that have been made, it's worth noting that we live in different climates (some artificial) and eat a different diet (much of it artificial) than did our ancestors. (I don't know what the acne rate is among modern-day tribal societies.) Tens of thousands of years aren't enough to completely rewire hormonal effects on sebaceous glands in response to a rather minor selective effect.
This may be a question trivial for you, but: Why is there variation inside a species? On some instances, you could argue that the Nash equilibrum is mixed (for example, different men prefer different physical appearances of women, so women of different appearance can coexist), but: What the hell is the evolutionary advantage in having zits?
Probably, it has something to do with genes of different types (all of whom have a good reason to stay in the gene pool by a mixed Nash equilibrium) mixing up and producing zits, but: Why should evolution, that managed to create eyes and brains, be unable to get something against this working if other members of the same species can perfectly manage to avoid them? Because such a gene can easily exist in individuals that don't have that particular problem (and I can't think of any adverse effects this would have), it should be able to spread even if not all members of the species have a particular problem. The disturbing thing is that I imagine a working fix without adverse effects to require only pulling some hormonal levers, not coming up with the complication that is needed to make a proto-eye better by a positive amount (so that the mutation can survive).