I think thewake fits quite a few of your preferences! It's not horror, and while there is metaplot it's not necessarily the main focus of the game, but other than that it meets them all. We have a few villain-type characters in there currently, as well, and even more scientists and inventors.

We don't currently have any other Villainous characters in-game but I know several players are familiar with the show and I'm sure they'd love to see anyone from it! We currently have a test drive going if you'd like to check it out.