Well, that doesn't really contradict itself, it's just that runes are not really a theme, at least not in the sense like biomancy or ectomancy are themes.
Biomancy can do anything that thaumaturgy can do, but you need living matter to base your spell on. Instead of magically picking a lock, you could supercharge your muscles and simply rip it apart. Instead of throwing a fireball to hurt someone, you make their blood boil. And so forth.
Ectomancy can track things, if you ask ghosts to keep an eye open. It can make a car malfunction if you convince a ghost to inject itself into the motor. You can do anything you like, but you need ghosts to do so. Without them, you have a problem.
Both of those are inherently limiting, runes are not. At least I don't see it. Which is probably what you mean by troublesome.
Is there anything besides "based on runes" he wants the magic to be? Like I said, there's not much of a theme in there inherently, but there might be if there's a bit more to work with. Sponsored magic could work, as well, maybe.
I've created a sort of modular runes set with a player to get away from modeling runes as magic. Maybe that's something for you. The idea was basically to assign a power to each rune and allow the player to switch them out using modular abilities. We went for 4 modular points and the player created sets of runes that thematically fit together to create power sets instead of having individual powers on each rune. It was mainly done to fit the character better, but maybe it's a route you could take here as well?