Even though this topic has already veered off course, I still want to throw in my thoughts.
After the Morning War, the Geth no longer saw the Quarians as a threat. They already had some infrastructure on the planet, and since they are all about efficiency, as AI are shown to be in ME, a planet with even minimal infrastructure is better than one with none.
They had no concept of the political necessity for the Quarian leadership to strive for centuries to retake the homeworld, to fulfill the biological necessity of the species. The Geth never planned to give the world back, and they saw their fleet, already on par with the Turians, as adequate protection against the Quarian fleet, which until the advent of Xen's weapon, Thanix cannons and the Korlus raid, was woefully under equipped to take on even a weak navy.
The Geth did not keep the planet out of malice or revenge towards their creators. They simply didn't care what the Quarians needed. Rannoch and the surrounding system was the most efficient place for them to build, and moving would waste time and resources when they thought their base of operations was suitably secure.