As long as we're talking about fleet system improvements, here's one I'd really like to see:
Factor in members' careers. Science officers could get minor discounts when putting resources into science projects, tacs get discounts for tac projects, etc. Create "departments" where the fleet can assign members to handle special projects for bonus fleet experience, similar to the doff system.
And another thing I'd like: Non-rank-based fleet roles. Being one of the leaders of a strictly-military fleet, I'd love to be able to run it as such. Roles like supply officers, responsible for acquiring, maintaining, and provisioning op-assets and such; maintenance officers, responsible for repairs and upgrades, etc. There is SO MUCH potential in the fleet system right now, and these are not hard changes.
Also, something that was brought up by another thread, a few more ranks would be nice. 10 ranks instead of 7 will add authenticity and flexibility.
I'd also like to see enhanced permissions. I won't pretend I know how difficult it would be to implement, but perhaps a system that will allow for permission modification on a member-by-member basis.