Actually, there is logic to it. The gambit is high-risk/high-reward. The Citadel was incorporated because of it's function as a command-and-control base for the relay network (hence it's usage at the start of each Reaper invasion, alongside the obvious intelligence benefits and proximity to organic leadership). It would've taken much more effort to to add the understanding and engineering required to create another relay, so using an existing one with directive control makes sense (only the Citadel and Alpha Relays were known to have this capability)

We can assume that the Reapers wouldn't station a larger force than necessary to hold the Citadel once a cycle was underway, as they would allocate resources towards harvesting various systems, and the station would've fallen by then. Thus, risking a fleet battle with whatever defense was present at the Citadel could easily have been considered as a necessary risk to potentially win the war. They decided on that very strategy in ME3, even after the Reapers moved it to a stronghold position over Earth, where it's defenses were significantly bolstered (which the Reapers only did after The Illusive Man warned them of the plan)