Think the changes on the whole make sense myself. Rose and Walker have tended just to be playing one game a week throughout the season and their efforts in getting up and down the pitch each match will naturally make them more tired than most. Plus one of Slovakia's biggest threats is Vladimir Weiss, and Clyne is much better defensively than Walker.
Alli hasn't played that well so far and it's right he's given a rest, and Henderson/Wilshere will give more natural left/right balance, which I would assume means we will play a diamond. Rooney is a bit of an odd one to leave out, but fatigue could be an explanation, as could Lallana's willingness to press in the 10 position.
Finally, Sturridge and Vardy have to come in for a chance. They changed the game for the better and in Sterling/Kane they will be replacing two underperforming players so far.