I do wish there were more 'support' villain options.
In our group, often one villain is not enough, but two are too much. Would very much like to see an idea about smattering the game with lesser villains capable of filling the hole...much like the option the Chairman has.
Instead of playing multiple villains, have you tried one villain in Advanced mode? Just curious, as it sounds like you're saying a villain in normal mode isn't challenging enough, anymore.
the Operative is not an "option" really, its part of the Chairman villain.
If you're talking about adding on a few guys who could serve as Heralds do for Arkham Horror, I wouldn't be opposed to the plan.
Still, I agree with Rabbit, I'm guessing that you are not playing on Advanced mode, because if you were, Omnitron would be about the last guy I'd want to have teaming up with the main baddie. I would reccommend trying that first before asking for additional challenges =p.
Actually, there's nothing about this that couldn't be done by anyone with some time (except the art maybe). Just make up a couple of mini-bosses you could toss into a fight if you wanted a different level of challenge. Omnitron's Prime Devices or Baron Blade's Battalion Leaders or a couple of new named Citizens. Give them some Operative- or Ennead-level abilities and put them into play when you first lay out the villain card. Sounds fun.