In other words, delete all caster classes and penalize hybrids? You do realize there are enemies strong in Element X, and every single mage has to at least dual-class, right? Not a fan.
For dual-class you are penalized by one point. You have two schools. Where is a problem?
Right here:
"For dual-class you are penalized by one point."
The concept of some restrictions for the skills you can learn isn't necessarily bad. The idea you proposed IS bad because it arbitrarily punishes anyone who is not a single-ability specialist and harshly punishes anyone who dares to take three abilities.
However, I can see a similar kind of restriction working with skill tiers, so that first tier skills only need a single point, Second tier skills need two points, third tier skills three or four points. So for instance, one point into Scoundrel will let you learn any of the Tier 1 Scoundrel skills you can buy at levels 1-3. At level 4, Tier 2 skills unlock and you'll need to spend a second Scoundrel point there to use those.
The difference is that one point in the ability is all you need for any first tier skills, you don't need two points to learn first tier skills.
Thus you can be a generalist with a lot of skills, but they are low-tier skills, and you'll need to invest further if you want better skills.
This will allow you to build a deck of low-tier utility skills, and encourage you to specialize into certain areas with higher tier requirements.
