I figure it'll be a little like what happened when FO3 came out, except to a slightly larger degree (since Skyrim is a new Elder Scrolls game): several folks got excited over the new game (FO3) and it's possibilities and started making mods for it instead of Oblivion. After a while when the newness wore off, things stabilized a bit: some came back, some didn't. I figure Skyrim will do that except to a somewhat larger degree: the new game will get a lot of attention for a while, and then things will equal back out.
I wasn't here when Oblivion first came out, so I don't know what effect it had on Morrowind's modding community in the short-term afterwards, but looking now, MW modding is still doing quite well (I'm reluctant to say thriving because I didn't see MW's modding community at it's height, so I can't compare).
I have noticed that the Oblivion modding forums don't seem to be as quite as busy as they were a couple of years ago before FO3 was released, but there's still a lot going on.