I'm going to stick my head out here and say that neither of those things are innovation. For me, an innovation is something that, once one game has done it, you want every other game - within reason - to do also. The portals of Portal and gravity of Galaxy are not such things. They are closer to what I would call 'gimmicks'. I'm not saying they're not excellently implemented and such, but still, they are not the kind of thing that I could reasonably want every FPS and every platform game to have.
To give another example, I think the Gravity Gun is one of the best game mechanics of all time. It's absolutely bloody brilliant. But I don't consider it to be an innovation, because I wouldn't want every FPS to have its own gravity gun. On the other hand, I would probably say that the complex physics system of Half-Life 2 is an innovation, because I could see myself wanting every 'real-world' styled FPS to have a complex physics system.
Perhaps I'm running on my own definition of innovation here, but for me Portal was innovative because of the fact that it was a first-person puzzle game rather than because it did some neat stuff with gravity. When I look at SMG, I don't see a great deal of innovation, but I do see a lot of original ideas, executed totally flawlessly.
Having said that, I'm not sure what I'd give best innovation to this year. Possibly Portal for the reasons I mentioned above.