Nah, I don't think if you're not going "Good vs Evil, with a good protagonist" you have to go "Evil because evil's cool." I think character's having more complicated morality's just far more interesting. I think grey vs gray is a far more interesting way to take it, because that's the way the real world is. When it's Good vs Evil, there's not really anything interesting being added there. If you have two sides facing off for reasons where either one of them could be the moral choice depending on what your own personal morals are, that seems far more interesting. Plus, we are talking about CYOAs, so choice should be a thing, and a choice between "Good" and "Evil seems far worse than a choice between two sides that both have a fair point.
I think you're misunderstanding my point, and perhaps I've phrased it badly. I'm not saying "Good is bad, Evil is good". I'm saying "Black and white morality, no matter which side you're on, is bad." "Good" is boring because it makes the entire conflict far more bland, as if one side is good, the other's bad, and you can't really delve into the moralities as a whole, plus, that's just not how the world works. Black and white morality simplifies things to such a great degree that it ruins nuance completely.
Alternatively, I quite like stories where you play as evil, but that's expanded on. Look at Eternal, for instance. You're clearly playing evil, but you get to actually develop that. The Eternal's a cunt, but his desires aren't "I serve evil! Muahaha!", it's "I serve order, even if it's with an iron fist", and "I have to come to terms with the fact I'm not special, don't deserve to be alive, and I want to be something, to be remembered, to be eternal." Those stories tend towards my favorite, when traditionally evil characters are expanded to be much more reasonable from their perspective.
So no, my main point would be that Obviously Evil is a bad thing, whether you're the hero fighting that or the villain fighting for it.