I believe with balance there is a sacrifice to be made with class/race individuality. I don't really see a huge balance issue in pillars of eternity. In BG series they used D&D 2nd edition. It was probably the most unbalanced system I ever used, but it was a lot of fun. The thief class was not useful in combat unless multi classed. They were a one shot wonder hoping their backstab would hit. That was the whole point though. They weren't a combat powerhouse. They were a thief that steals, hides in shadows, disarms traps, and opens locks. It's one of the things I miss from that system. Every choice you made had a huge impact.
Choosing a race as melee that had less then 18+ strength for a melee class made a huge difference. I wouldn't make a system like D&D 2nd edition (especially the overpowered dual and multi classes), but I find pillars of eternity to be a little lacking in terms of choices you make like being a Orlan making being a fighter difficult (which it doesn't). I would have liked to see something like Orlan's having -8 strength, +6 dexterity and + 2 perception or something of that nature. Basically something that would have a major impact.
I also think balancing had too large an impact on attributes. For instance might increases the damage and fortitude of everyone. What exactly is might though? If it refers to a characters strength then it should only impact damage for heavy melee weapons. How does might impact a characters spell damage?
I still love the game and I think it's a better system then what I've seen in games of late, but it definitely sacrificed a lot of uniqueness for the sake of balance IMO.