I support the Imperial Agent doing missions for either the Empire or Republic depending on their choice at the end of Act 3. I guess the Neutral Agent could get a 3rd choice like "follow up on the lead that both sides ignored and discover a Hutt conspiracy with the Mandalorians" or something like that.
The SI definitely needs to have a more political aspect to it. As an SI I always felt like my storyline was Indiana Jones meets Nathan Drake. What I wanted was Palpatine meets Thrawn