I also was under the belief that Wolverine and the X-Men was a continuation of Evolution. Thought, the head writer of WATX, Greg Johnson, let me know that it was not their intention, and they tried really hard to set it apart from Evolution.
There is a rumor that there will be a new X-Men series, but nothing is confirmed. I can tell you that Greg Johnson knows nothing about a new series, and even though he was well established in the Marvel animation world (working on shows and animated films), he's been kept out of the loop. Marvel seems to think that Man of Action (who produces Ultimate Spider-Man, and jumped in half way of the second season of Avengers: Earth's Mightiest Heroes) is good enough for them. :-/
There has been talk that the new Avengers Assemble series takes place after Avengers: EMH, and since EMH is in the same continuity as WATX, there may be a good chance that a new series may pick up where WATX left off (fingers crossed).