It's crucial not to forget about the Allied Spirit - it all but doubles your Rune Point cap, and is a really big deal in general these days. Still, the cap is still there, just later. (You can milk some more out of being an initiate in multiple cults, but even then, it's just a matter of time before you run out of space for new rune points. Except perhaps barring illumination, at which point you can go wild with cults.)
By the point you're up to 40 Rune Points or so, the GM Book should be out with Hero Level abilities, too. That will remove much of the cap.