According to standard Republican scripting, Rove will be departing the White House to spend more time with his family. That is code for behind-the-scenes turmoil. There has been some talk that Cheney and Rove were having disagreements, and one possible point of contention could be Dick Cheney's push to bomb Iran's nuclear infrastructure. Perhaps Rove does not want to be present for that upcoming debacle.
Other possibilities include the fact that Rove is hoping to avoid any subpoenas from Congress concerning the firings of US attorneys, or that Rove will just be moving to a stealth advisory position, where he can continue to work behind the scenes without accountability.
The most likely reason behind the departure is that Karl Rove thoroughly botched the 2006 election. Everything from the incidents of vote caging to the voter suppression techniques used in places like Florida and Ohio were Karl Rove productions, and all of these failed miserably. So it is just possible that Karl Rove is leaving because his bag of tricks is empty, just like Bush’s cranium.