I'm not a fan of the Vasudan part in FS2, however, I would say to you to leave them in as it fits nicely into the original canon with officer exchanges. If it enriches the story then definitely leave it in.
I don't like going to the cinema for several reasons, but the one I highlight is the sometimes shortened version of the movie. If you want to get to see extra scenes and such then you have to buy the director's/extended cut. This annoys me because I want the full story the first time. Films that I think have benefited from those scenes for extra depth include Aliens, Terminator 2, Independence Day and Dune.
Dune is subject to massive freaks of editing as the original cinema release had massive chunks cut from the film. An extended version was released, but it did not include everything. A full director's cut was released which included everything and added something like 45 mins (iirc) to the original release. When you compared the original release to the director's cut (which David Lynch hated and would not allow his name to be associated with it) you could see how some scenes had changed position in the film and altered the arc, whether for better or worse is just a matter of opinion.
I would say to include everything that you have done which adds depth to the story. It is your story to tell and I want to experience all of it! The only time I think something should be cut is if it erodes the continuity in you story.