Originally Posted by cherokeesam
Good points, and good analogies.
Maybe it could be a situation similar to what IM3 seems to have, where you've got two main villains, and both seem to think that they're the one in charge (Killian and Mandarin). You could have Zola/MODOK as an evil genius rogue AI in an android body, working with a more human ally like Zemo or Lukin or Strucker who's intent on bringing the Bad Old Days back.
That would be the ideal solution.
Then we could have Chris Pine's Kirk dishing out some logic and causing the rogue AI to self destruct on his own because of some directive he can't disobey. Wait... wrong franchise.