Implementing a faction with a different motive than a simple "we're evil" brings a different perspective to the world. The Institute is presented as an antagonist faction but since they care more about business than ethics, they could end up in the same team as FIST on occasion. Only if it is profitable, though.
The enemies are interesting and fit a specific role, all with paranormal powers or characteristics. They don't really have a "classical" soldier on their roster but it might simply not be their specialities.
I like how there is a compatibility section in order to implement the Institute in narrative settings.