Actually, I suggested 9 PrC levels so that each power would have 5-steps of progression.
It's hard for me to imagine how you'd make it 9-steps without going overboard with the numbers.
Also, it's not traditional spellcasting and I see no reason why it should resemble traditional spellcasting.
Don't put a daily cap on it. Let the runic reserve dictate everything and let the players manage their resources.
It's just up to you to make sure no specific strategy is routinely the winning ace, because a lot of the game tension comes from having to make the right decision according to the changing situations.
I vote against.
You see, not everybody has the patience to juggle the incarnum system with all the involved terminology (I always found it tedious and didn't feel like bothering).
Come to think of it, in concept rather than pure mechanics, incarnum seems like a combination of traditional magic and runic magic, but gaining partial benefits from each.
To me, a clear separation is a good thing. Either you have more versatility or more available access to your powers.
I present them as they pop.