Cool idea, an antagonist recast would spice the old content up 
And I'd love to see the Rogues Gallery show up at Radio/Newspaper missions as well. Who the hell wants to fight Clang-Clang-Clang or Archon Leery? Make it Flambeaux and Dr. Graves!
A while back I had the idea for your personal Arch-Nemesis to be added to the game, probably never mentioned it.
the idea being that around level 20 or so you qualify as "big time enough" that you attract the attention of a villain or rogue (if you're a villain, vigilante, or hero), a vigilante (if you're a rogue or villain), a hero (if you're a villain), or a handful of other characters regardless of alignment.
Hero - Villain or Rogue comes after you, most likely villain.
Villain - Hero, Vigilante, or Villain comes after you, most likely Hero.
Vigilante - Villain or Rogue comes after you.
Rogue - Vigilante comes after you.
For our example, we'll say you're a hero and your arch-nemesis is the randomly chosen "Tarantulax," a giant mutant spider with axes on the ends of its legs, very scary.
You're doing a typical hostage rescue mission, and just as you rescue your kidnapee, and start heading back to the entrance, you happen to notice someone with superspeed heading towards you from the exit you have to take to get out of here. It's tarantulax. He charges after you and initiates the fight, using a few powers to try and stop you or slow you down. If you escape with the person you're trying to rescue, whether or not you beat him, you win. Otherwise, Tarantulax will beat you, automatically become your first nemesis, and just to rub it in he'll steal the person you're supposed to rescue and leave with them. you get mission completion status (because another hero rescued the person from Tarantulax), but from now on Tarantulax will harass you when you're doing missions. If you beat him, or if you get away, Tarantulax goes away and never bothers you again, but other characters from that rogue's gallery will each get their chance to take you down, making you their arch-nemesis.
Eventually you will, at level 50, get the chance to make a final confrontation with each of your nemeses, and when you beat them (eventually), you can replace them with someone from a list that you get to choose, or even create custom nemeses.
For example at level 50 I might choose to make my arch-nemesis the duke of pie, and I go into the costume editor and make a completecostume for him and a few quotes and such.
you could have it all
My empire of dirt
I will let you down
I will make you <3
With my luck the Guild would assign me the Monarch, lol.
Sorry for the sarcasm. I actually like the idea of having more personal big bads.
I would like to see the Rogues Gallery expanded on.
Ultimately, what I'd like, is to have random named villains appear in all manner of missions, instead of just tips.
Expand the group to have 20 or so more costumed villains/heroes and write code that allows them to attempt to sabotage any mission you are on, except for TF's/Trials.
Wouldn't happen all the time, but every few missions or so, depending on level, a small time crook or big-bad from the Isles would either replace the standard groups endboss or appear mid-way through the mission to attempt to finish before you. By kidnapping the one your to recuse/ grabbing an item first, etc.
So, you run Frostfire and the mission runs like normal.
Couple of days later you run Frostfire but this time Mangle shows up and beats you to the key, forcing a showdown.
You grab a mission to defeat a random freakshow boss from the radio. Only Shock Treatment beat you there and took him out first, now you've got to get the info from her instead.
I understand the code might be impossible to write/ take to much time etc.
However, I wanted to throw it out there anyways!
Maestro Mavius - Infinity
Capt. Biohazrd - PCSAR
Talsor Tech - Talsorian Guard
Keep Calm & Chive On!