You know, it's amazing how often I feel like I don't really understand everything that's going on in the game in terms of mechanics. Luckily, I feel like the basics are easy enough to get a hold of. In some ways, I think I still prefer how a game like Titan Quest handles skill progression just in terms of sheer simplicity, but at the same time, I appreciate what Sacred 2 is doing, and it's certainly unique.
I've still yet to screw up a skill by adding too many runes to it, so I think, for the most part, if you stay under the threshold of the "level without penalty," you won't totally kill regen times. That is, I've yet to add a rune and immediately think my regen times have changed considerably.
I think what they're going for at this point is that just adding a rune isn't a penalty--it's a basic progression of the combat art that is meant to "keep up with" the character's progression through levels. So, just as a spell in other games would cost more mana at higher levels, you're going to see a slight increase in the casting time at higher levels.
The penalty seems to be to prevent people from going crazy with a skill at a low level. It makes sense based on the mechanics--higher levels of a spell in other similar games would be locked at a character's lower level. This is Sacred 2's way of keeping your combat arts in check.