This made sense right up to Cronos Station.
Before talking to Vendetta I had assumed the following :
In previous cycles the Reapers arrive at the Citadel from Dark Space taking galactic civilisation completely by surprise.
The Citadel cant be defended from this attack because the reapers are already there. No counter attack possible, its already too late.
The Reapers seize control of the Mass Relay network.
Entire regions of space are isolated from each other while a galaxy wide communications blackout ensues ( comm buoys are as reliant on the Relay network as spacecraft are ). Even if galactic civilisation is unified (an unlikely scenario) any resistance will be uncoordinated and severely limited.
The Reapers can then mobilise overwhelming force at will and methodically harvest the galaxy system by system.
This is the Reaper's traditional MO as outlined by Vigil on Ilos.
The Protheans via Shepard stopped this in ME1.
Without the element of surprise an attack on the Citadel is pointless.
The Citadel retains it's strategic value but it is no longer a viable target due to it's impregnable nature.
The Reapers probably couldn't take control of the station without destroying it in the process rendering the whole enterprise pointless.
This is why the Reapers ignore the Citadel throughout ME3 and have had to fight a conventional war on several fronts at once.
The problem with the plot is caused by the Reapers taking control of the Citadel after Cronos Station mission.
I think this was done so the final battle could take place on Earth.
The logic of the narrative dictates that upon learning that the Catalyst is in fact the Citadel and that the Illusive Man has informed the Reapers of this the climatic battle with the Reapers should have been at the Citadel. Earth is irrelevant.
The Allied Fleet would have had to get the Crucible in place while the Reapers would have tried to stop them. Given that docking the Crucible requires the opening of the Citadel arms any attempt to use the Citadel against the Reapers would have simultaneously left the station vulnerable to Reaper forces. The end battle would have seen the stakes for both sides raised higher than ever. I think this would have been a far better final act than the 'TAKE EARTH BACK!' finale we got.
To summarise :
The Reapers avoiding the Citadel is not a plot hole but the Reapers taking the Citadel to Earth is a huge plot hole.
This was unnecessary from a narrative point of view and seems to have more to do with Bioware's pre launch publicity than the story.
I feel that the narrative was subordinated to a marketing campaign. Ideally it should be the other way round.