What specific "hybrid" are you saying is underpowered? If you're trying to use two or more of the three main stats to do your base damage and CC, then yeah, you're going to have problems. But that's sort of like complaining that a character who gets to level 5 in bows does more damage with a bow than someone with 3:3:3:3 skill in 4 different weapons categories can do with whatever weapon they decide to pick up.
If you instead make a hybrid that focuses on one of Str, Dex, or Int, and then maybe dabbles in one of the others, you'll be fine. A truly balanced hybrid gives you versatility, not power.
I'm talking about penalties beign too severe when you choose 2 schools that have different boosting attributes and level them evenly. If those penalties would also affect hybrid mages like pyro/geo or hybrids like scoundrel/marksman then it would be balanced.
Why does a 4 man-at-arms/ 4 Hydro suffers from low hit-chance, unreliable CC, high cooldows and can't invest properly in Speed or Con while a 4 Pyro/ 4 Geo would have none of this?
I can use your own logic: Why does a guy who learns Fire(5) and Earth(5) magic can have the same efficiency(with Fire spells) as a guy who focused only in Fire(5)?
The one who specialised in Fire alone should be better at it, isn't it? As of now it is not.
And as I said, versatility isn't good when you fail too many CC or hits. For versatility to be good it has to work. Mages can have the versatility of 3 different Schools and would not have any of the issues mentioned above. Also true for Scoundrel/Marksman.
Maybe you are failing to see that spending those points it's already a penalty, because you can't fill both roles per turn, only with high level gear gving you speed. A pure char would be filling 1 role per turn and would have those points spent in weapon dmg or saving throws, while the hybrid would have the flexibility to choose wich role to fill in a round, but without that extra point in dmg or savin throws.
I believe that double attribute builds should be more reliable, after all you're spending points that could be going to BB or will or weapon damage.
In some way I agree with you that it just makes sense that a "split" build should not be as strong as a pure build. I just believe that the benefits and penalties are badly implemented.