Fair enough, Zhent gives you a reliable means of sneak attack...after waiting around 8 levels with sneak attack and not much to work it with.
I don't understand why you're talking up "things the Fighter can do that aren't damage" in support of the sneak attack variant, when trading feats for SA is literally trading options other than doing damage for more damage.
And what is Thug adding to the Zhent/SA combo, other than not actually stacking with it due to replacing the same class feature?
4 + Int skill points on a class with no real use for Int still does sweet FA. If you're playing a fighter, you're not going to be a skill monkey. Just accept it and focus on the handful of important skills useful to you.
Thug is horrible because you lose one of your front loaded bonus feats for a whopping 4 new class skills -- only one of them actually good (Bluff) - and some more skill points. You swap a genuinely useful feature for the ability to still be mediocre at something. Even worse, losing the feat and prof. makes it incompatible with other fighter variants, like Drow and Sneak Attack Fighter.
As for sneak attack...If you get your stance via Swordsage dip, then it is a class ability.