I don't understand why the Emperor would put house Etreides in charge of the most valuable natural resource in the universe, if he was worried they were getting too powerful. Seems counterintuitive, is there some reasoning behind this?
Basically:
Atereides had become too powerful and the Emperor was afraid of his influence.
Harkonnens would never succeed a direct attack on Atreides home world, heavily fortified.
So the plan was simple: give Arakis as a gift to the Atreides, make it impossible for them to refuse. Atreides are forced to leave their fortress and on Arakis are much a easier pray. Harkonnen can finish their feud with the Atreides and the Emperor can claim that he had nothing to do with it.
Arakis was just a pretext to place the Atreides in a vulnerable position in a way that they cannot refuse.
Remember Game of Thrones and Ned Stark? That was the same situation and GoT "stole" a lot more from Dune than that.