All it takes is a good writer to turn a throwaway villain into a compelling character.
That is true, however with the way Bendis introduced most of those throw away villains, as one dimensional jokes, it will take a lot of skilled writing to make them compelling enough to headline their own title. First impressions are important and the first impression Bendis gave us most of these villains were that they were one dimensional losers, you almost have to come up with reasons why these guys are supposed to be dangerous enough that government would want them as black ops agent, when Spidey easily defeated them in the space of page.
One of the things that made the Thunderbolts work in the 616 universe, is that the team was made up of villains people were already familiar with and put into a different situation then what they normally appeared in. Considering that most of the villains in the UU are either dead or just jokes, there are not a lot of choices in terms of familiar villains to the readers that could be members, not like in the 616 universe where these villains have been around for decades before becoming Thunderbolts.
Regarding these throwaway villains, the writer would have quickly establish why we should care about these villains, giving them more defined personalities, giving them a reason why they should be regarded as dangerous, essentially justify their roles as the headliners for an Ultimate Thunderbolts title. This would reacquire a writer who is skilled at taking B and C-list villains and making them more interesting and threatening, many writers in the UU have done the opposite taken B and C list villains and made them more pathetic and less developed in the UU.
However a Ultimate Thunderbolts title could be an good way to introduce 616 villains who haven't been used in the UU before, I think of a way to use Helmut Zemo in a title like this.