I agree that they could use some more tactical diversity but I think that you’re exaggerating a bit when you list problems with them.
Apart from throwing axes resistances make sense, they have no flesh or organs to pierce nor veins to cut. You only damage the bones and it’s not easy to hit those with a sharp point. This has been an understandable and accepted staple with various fantasy games for literally decades.
I assume that the inability to tell whether a hammer pierces or crushes is a joke.
You say that they make “builds” useless – but 1 or 2 perks don’t constitute a build. If you have a generally good bro he can do allright, maybe give him a different weapon, that’s all.
If, one the other hand, you’ve made a fearsome-crippling-executioner-dagger specialist you’re simply being faced with the flip side of any specialisation – while doing great against some enemies it performs poorly against others. You wouldn’t call orcs broken just because a swordmaster can’t crack them, now would you?
At any rate, that’s what you have the reserve roster for – keep your builds somewhat varied and simply switch bros based on their effectiveness in each battle.
Also, skeletons resist missles – their armors don’t. They have more armor than HP so just equip your rangers with crossbows and watch the skellies mostly melt before they even reach your line. Then switch xbows to longaxes or billhooks.
As for specific options let me point your attention to the fact that they often miss either body or head armor, while usually carrying shields. Flails with mastery completely ignore shields and let you choose whether you want to jit head or body. Do you own math.
Of course later you meet fully-armored skellies but it’s the same with humans and orcs, so no big deal. The difference being that decayed shields are trivially easy to break, giving your hammer much easier task.
Also from my observation they have somewhat low accuracy, they rarely hit my shielded tanks. So just suit up and grind them to bonemeal.
P.S. As for seeing through bushes – they are magically reanimated dead. They don’t HAVE eyes. Why would you assume they “see” the way the living do?