The Reapers couldn´t bomb the Citadel until it yields, it houses their central intelligence. 
An explanation why I didn´t shut down the relays anyways would have been fine though. Something like: The prothean hacks allowed the Council to shut down Citadel control over the Relay network after a heated debate where no one agreed to let the Council control the network together. Catalyst got shut out during the process. Could have fought the tinkering but then it would have been obvious that there is a hostile AI on board and as far as we know it has no internal defenses. And the Reapers are pretty bad at fighting wars. they never fought one. Their MO was "surprise attack, cut off communications and transport, then mop up."They are good at ambushes but every ship is more or less irreplacable. They attacked with overwhelming force where they expected resistance and stretched themselves thin in places they didn´t.
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