The stories and zones were written in a way to convey progression of a character from the bottom gutter of the Zig to the same table as Recluse. Each zone you meet another contact that elevates your character to a higher point in the story. At the end you're taking on the major heroes in the game and even Recluse himself. It's a fantastic way to enjoy the game and I think it is good all on its own. With the advent of Archetypes no longer being locked to blue or red side (along with faction switching being instant), there's not really a side anymore (except Gold side!).
As to what could increase player population? Well I don't see much "City of Villain" anywhere on Homecoming's forums, discord, social media, or Wiki accounts. It's City of Heroes and that's what people probably think first to try. Maybe make some more CoV logos and slap them on things? In game, I'll just say that being a Villain doesn't mean what it used to mean. You're making choices that are mostly just Vigilante writing outside of the real dark contacts. It's always about making cash until you get to Grandville, then it's about power. Maybe that's what I said is worth trying, make being a Villain mean something.