I'll tell you what Facebook innovated. (You're not going to like it, though, because we tend to think of innovation as synonymous with "progress" and progress is usually measured in terms of end user utility. And what I'm about to say is totally not that.)
Facebook somehow had a website that was popular (that's not a part of the innovation, but it's an extremely important prerequisite) and then got a million other websites to embed references to Facebook resources into theirs, like Google did with Google Analytics. Since most browsers, by default, are happy to load any embedded resource referenced on a page, that gave Facebook an incredible number of "hits" from diverse sources.
Most classical (i.e. naive) 1990s-thinking web people would see these "hits" as totally valueless, because they're not pageloads, they aren't showing ads that you got paid to run, or whatever. The clever people, though, saw that you use this sort of thing with a cookie and combined with referer[sic], to build marketing profiles.
The mid-late 1990s clever people knew that too, but their references were ads themselves (e.g. doubleclick). They had to pay to get other webmasters to embed this crap. Nobody is going to embed a doubleclick image (i.e. an ad for something) unless you give them money.
And webmasters embed these things for free, because they feel they get something out of it. With Google Analytics, you get the reports and analysis. Sure, you could get a lot of that from your own logs, but not all of it (Google knows some things about your visitors, that you might not, and this is their business, they're able to "keep up") and GA is easy and there and waiting for you. With Facebook like buttons, discussions, etc, webmasters are counting on the popularity of Facebook, to make it so that people who use their own site, will generate events on their Facebook profiles which will be seen by other Facebook users who don't use their own site, and maybe someone will curiously click through and you get a new visitor.
You gotta give Facebook some credit for that. I get how Google turns their spying into money, but I still don't really understand how Facebook does. (Apparently Wall Street doesn't understand it either, judging from the ever-falling stock price.) But there's probably an angle, and however it can be used, Facebook has very successfully put into place at least half of it already. Getting so much of the web to embed your script or iframe (and without having to pay them for it) -- holy crap, I totally can't imagine that happening fifteen years ago.
So it's innovation. Just not the kind users like to see happen.