The current system has flaws, but it still infinitely preferable to a system in which your skills only have a chance to work.
If you have an ability that has a % chance to work, it is not reliable. If you need that proc to win the fight, you've already screwed up and are now relying on chance to win the fight. If you don't need that proc to win the fight, it's effectively worthless and you might as well go with a harder hitting skill to win the fight more quickly. This is true not only in this game, but ANY similar game. (In Pathfinder, if I'm playing a caster, I will NEVER rely on spells that allow a save and have zero effect on a successful save; any spell I cast will either be one that doesn't allow saves, or that still has a useful effect on a successful save. Every spell cast will be effective; the level of effectiveness will vary, but I will never have my action be wasted due to random chance if there is a viable alternative. Same concept.)
Control abilities aren't always useful in this game, but I'll take this system every time over "XX% chance to stun/knock down/whatever".
As for issues with the current system... the biggest issues are the split armor types and the lack of physical resistance. The system encourages parties to focus on a single damage type, and the fact that there is elemental resistance but no comparable stat for physical damage means that physical damage will typically be a superior choice. I also don't think armor should block non-control debuffs, but that's a less severe issue.
I also think it would be less of a problem if you had more pure damage abilities or abilities that dealt with breaking armor specifically. Most of the Warfare and Scoundrel abilities focus on utility or debuffs, so breaking armor is a matter of pure attack damage. There are some easy alternatives though.
Warfare: Armor breaking skills, that deal no damage to vitality (even if armor is already down) but do increased damage to physical armor. Overpower has kinda the same vibe, but is too limited and too binary.
Scoundrel: The sneaky school, it does have some piercing damage but should be able to apply some of its debuffs through the armor; Ruptured Tendons already does this, just expand the idea. Chloroform is a pretty weak control, so letting it bypass armor doesn't feel like it would be overpowered.
Universal: You could also let any ability which applies a control blocked by armor do bonus damage to armor if the debuff fails. Knock Down failed because physical armor is still intact? Extra physical damage! Freeze failed because magical armor is still intact? Extra cold damage!
Alternatively, you could rework the school abilities themselves. Instead of buffing damage, Warfare and the Elemental schools could grant bonus damage against armor, or extra bonuses against armor.
There are a lot of different ways you could take the system, but rather than consider it a failed system, I just think it's a bit incomplete. Armor's a major part of battle in this game; you want yours intact, and you want to break your enemy's. There should be more abilities and skills to deal with that directly.
