One thing I'd love to see Mongoose do is a) really expand the hull design library of the setting (FREX the Feddies really only have the FF, DD, CL, NCL, CA, BC, CV and DN hull designs...how many different classes of ships were fielded in FREX WWII?), b) incorporate some of the "grey" area ship designs (like the Surya class, a prototype Reliant class, and not one I have ever seen in an official publication) and c) incorporate some of the better (really all) TOS era FASA ships. The latter two points might be going a little too far, but one can hope...
Damon.