You have completely confused 2003/04 with 2004/05 mate. Not sure how, but you have.
2004 when Rooney left was immediately after Everton finished 17th, with scandals in the paper about Rooney visiting brothels. Rooney had fell out with Moyes over it, blaming him for leaking stuff to the press (later found to be untrue, and I wonder who did leak that stuff to the press, perhaps to force through a profitable deal?), plus Rooney had had an agent in his ear for 18 months telling him to move (so that the agent could pocket a vast personal profit in the process) and had a media clamouring for him to leave Everton to further his career. Plus Everton desperately needed the Rooney money as the club's finances were a mess.
2005 - WITHOUT Rooney - was when we qualified for the Champions League.
As for the club's respective positions now, they're TOTALLY different than in 03/04. We are challenging at the top. Man Utd aren't challenging for the title, they're 8th, 6 points behind us, and we've already beaten them. They also have a different manager.