I always felt like CoH suffered from weaknesses in the character stories. That is, you never really felt like your individual hero was an integral part of Paragon City. Sure, you fought gangs and villains and whatnot, but you were always just one of hundreds going after the same gangs and working with the same dispatcher or cop.
What I would love to see are NPCs in Titan City growing around you and your character as you advance, and that would be so incredibly prevalent in having your own Rogue's Gallery. I'm talking about villains you witnessed the creation of, or maybe were created as a result of your own actions on a mission. Villains that keep coming back, that know where to hit you, and that actually threaten your ability to complete your missions when they are involved.
Put yourself in Batman's boots here. Imagine you're waist-deep in a criminal investigation, looking over a series of murders. Suddenly you turn over a dead body and a knot of dread rises in your heart as you see a contorted rictus grin on the corpse's face, and a card stuck to his shirt that says "HA! HA! HA!". And you know it's the Joker, and you know things just got infinitely more complicated and dangerous.
It's that feeling that I would love to see emulated in a super-hero game. There need to be villains that mean something to you, that you're a little apprehensive about, and that more than anything, you want to bring down.
Anyone else feel like this?