One of the challenges in RPG design is, of course, the system. To my mind a 'good system', from a design perspective, is one that delivers on the promise and premise of the setting. It should also be cleanly written and its mechanics should reflect the intent of the designers in terms of probabilities and character progress. There is a lot more to it than that, of course, but that is the core principles.
Henchmen is our 'getting our toes wet' project, so it was always going to be a supplement rather than a full game, and thus is using a pre-established system. I thought that Fate was a good go to mechanic, firstly because I had written 'homebrew' campaigns for Fate before, but more importantly its narrative character based ethos and stress and consequence mechanics fit with my vision of how I would like Henchmen to play.
I always envisioned that a central theme of any Henchmen campaign could be the characters' journey from mere underlings through to full villains. Fate's milestone system for character growth works better to represent this and an 'XP' based system
Stress and consequences are a great way of modelling all the obstacles, disasters and misfortune that come the way of a uniformed goon in a way that's fun to role play not just roll play.
In terms of future projects, I will doubtless visit Fate again, though the studio is considering making our next project a stand alone book, rather than a supplement. The studio also has its own dice mechanic in development, but as it is custom designed for a much larger project it may be a while before we shall be using it.