We know the Catalyst "lives in the Citadel" and that it is "a part of him", it might sound stupid but we don't really know if he has any control over it, evidence suggest it doesn't as unreasonable as it sounds.
Even if it could, if doesn't want to, there's a reason why it allows Shepard to use the Crucible. The cycle is weakening, the organic civilizations advance one step at a time to stop the Reapers, this time they ecured the citadel, stopped a new Reaper to be built and unified against them, also they now possess a weapon potent enough to destroy the Reapers, his solution isn't going to work for long even if he wins this, the Crucible creates "new possibilities" and the A.I. let's Shepard decide their own future.
Destroying the Reapers will eliminate the cycle and let organics self-determine their future but with the possibility of being destroyed by a technological singularity.
Synthesis fuses organic and synthetic life to end the strife, but this ending is so futile I don't want to start thinking how wrong it actually is.
Control is arguably the best one, Shepard controls the Reapers, and, if a singularity threatens organic life he/she could presumably stop it using the Reapers.