I think there's been plenty of innovative ideas just within the d20 community.
In the beginning, everybody said, "oh, it's just D&D without the name. All it can do is fantasy."
Then came Star Wars and Spycraft. Two non-fantasy games (ok, maybe SW is fantasy) that d20 worked pretty darn well for.
Soverign Stone's magic mechanic, mentioned earlier, was certainly innovative.
I think creature templates were fairly innovative. A fairly reliable and quick way to modify existing creatures with similar backgrounds and abilities.
Of course, we haven't seen Monte's book yet, but the prestiege (sp?) races sound innovative.
How about new stories? Midnight. Usually the PCs are all about keeping the evil at bay before it gets too strong. In Midnight, the stuff has already hit the fan and somebody left the fan on "high". That's certainly a departure.
Just because there aren't new rule sets springing up every few days doesn't meant there's no innovation.