@Gorb: Taking Health/Happiness; both can be gained from buildings (both limited by local pop), both can be gained from tiles (small tweak here - Health tiles are spammable but local, Happiness tiles are not-spammable but global), can be gained from virtues/policies. They are largely gained in very similar ways - the differences are numerical rather than mechanical.
This is mostly what I mean by innovation within Civ - new mechanics. Skin changes, name changes, numerical changes, they are just tweaks. Mechanical changes (like the Health/Happiness tiles) can be part innovation, part tweak - interesting, but not as much as a new mechanic would be.
I am also happy to see old mechanics brought back in if they mesh differently in the new metagame - so SMAC's alien mechanics would probably be quite interesting in Civ BE, probably way more interesting than aliens sitting around a nest doing very little. The aliens we have in BE are really just tweaks on Barbarians, but with some stuff taken out (like actually attacking your cities, capturing workers, scaling with your civ, etc.). I don't really see the aliens as an innovation, which is sad when they are meant to be a large part of what the game is about.
Basically, using current things in slightly different ways may be innovative in some sense (the new way is new), but it isn't an innovation. Example, I usually throw a ball with my right hand/arm; I could be "innovative" and switch to my left - but it isn't really a innovation, its more just a tweak. Kicking the ball would be part innovation/part tweak, however, having to fight off gremlins at the same time would be a more interesting addition (well, at least in my opinion) and be more of an innovation.