There is nothing given to use saying the Enclave had trouble getting it working. They could have simply destroyed the citadel long before the BoS got Optimus Prime Working.
The fact they didn't use it right away is evidence they had trouble getting it working. Liberty Prime is destroyed outside the Satelite Relay Station which was originally used to aim their orbital bombardments before control was transfered to the mobile base crawler.
Why didn't the Enclave take over the citadel before the BoS got to DC. They would have known about Prime being there.
The destruction of the Oil Rig would probably have destoryed most of the Enclaves records so they might no longer have access to all necessary information. Eden for example doesn't know why the previous plan failed simply that something obviously went wrong. This helps support that the old records from the oil rig are largely incomplete.
The surviors having only just arrived might not have considered it worth it to fight through the robotic defenders inorder to reach a robot nobody could ever get to work. After all there was no one in Capital Wasteland who could get inside so why bother until it was necessary? The Enclave does enjoy biding its time, they arrived on the mainland soon after the war with unity was over, but it was decades before they really became active.
Then Lyon's rolls in one and snatches things out from underthem. By the time a need to rush became apparent it was already tolate.
Why is it that the "graveyard" scenario does not play out. We were led to believe that it would kill pretty much everyone really fast and yet it does not happen. This makes the entire point of the Enclave's plan (Eden's plan) pointless.
Why does Augustus Rebel against Eden and then turn around after that and say things that still show him as loyal?
He doesn't trust the LW and believes its best to eliminate the threat. Many people commit treason in the name of protecting the nation there supposedly betraying. Chef Hanlon falsified intelligence reports because be believed war with the Legion would eventually lead the NCR to ruin. From Autumns perspective, trusting boy/girl who the Enclave tried to kill, caused the death of his/her father, and stole the lifes work of his parents sounds like a bad idea. He wil protect Eden and the Enclave even from themselves.
Why does the Enclave make a water born FEV virus and not just try their plan from Fallout 2 again? It would have worked so why would they go for Eden's watered down version?
Lack of proper equipment and probably time. Raven's Rock doesn't have the resources the Oil Rig did, so trying to generate the massive quanities necessary and the delivery system to pump it into the jet stream would take to much time and probably require construction on the surface that would attract attention. And considering the plan was disgarded maybe the Enclave themselves were no longer all immune to it either. The original toxin didn't discriminate and the Enclave required vaccine.