"Omega is described as "the Terminus Systems' dark, twisted counterpart to the Citadel.""
"Today, Omega is a major hub of narcotics, weapons, and eezo trafficking without even a pretense of civilian government or military control. "
It also controls access to the relay to the collector base and which is something that Cerberus controls. Cerberus alone considering it a major asset is enough for the Citadel and/or Systems Alliance to consider it a worthwhile target.
http://masseffect.wikia.com/wiki/Adjutant
http://masseffect.wikia.com/wiki/Lystheni
http://masseffect.wikia.com/wiki/Mass_Effect:_Invasion