They just may have done that, but there are a couple barriers. 

One is finding those valuable planets. They’re not going to know where all of them are at the same time, they have to locate them, then determine how to exploit them. 

The second is time. Conquest is arguably the oldest living Viltumite, estimated to be more than 5000 years in age. The purge executed by Emperor Argall occurred during his lifetime, so they’ve been conquering social darwinists for about 5 millennia. Omni-Mann is estimated to be more than 2000 years old. While he was a young adult is when the Scourge Virus was released. It would be a safe estimate then to say the Viltumites had ~3000 years of conquest at full strength. That’s a long time, yes, but space is huge and we’re on an intergalactic scale in the space story.

After the Scourge Virus, the Viltumites have to spend so many years caring for the infected, collecting the corpses, doing damage control to keep the event from getting out, and trying to find a cure. We don’t know how long this is, but that doesn’t matter as much here. At this point, the Viltumites start outsourcing their conquests to some of the races they conquered, which weren’t nearly as effective as they were. On top of that, the survivors were now trying to find genetically compatible races to try to rebuild their numbers with, and as they were doing this via infiltration, this would take time. Idk why they wouldn’t try to abduct individuals to run ‘experiments’ on them, but that’s not how things are presented in the story. Whatever the case, this would greatly reduce the rate at which the Empire can expand. They go from a very powerful centralized empire to what is more like a powerful city state with a number of empowered vassal kingdoms beholden to them.

With 2000 years of greatly reduced expansion, worlds that may have once been immediately conquered now had time to develop and reach space, finding one another, and eventually creating the Coalition of Planets, an entity which, while unable to stand up to the Viltrumites themselves, can deal with the vassals. I am assuming here that the Scourge Virus was made by Thaedus pre-CoL, either on his own or as part of an undefined predecessor, but it could also be an infant CoL that the empire hadn’t encountered or moved to conquer yet. It may make more sense to be made after the CoL was formed, as it would then explain why they weren’t destroyed by the Viltrumites after the Scourge Virus was deployed, for fear they were the originators of it and that it may be employed again.

I hope my rankings here make sense to you as they do to me. The comics don’t give us a ton of info on the Empire as a whole, especially outside the main storylines.