Being able to create missions for allies.
     AIs do it, and the components are simple... (choose a goal and a specific reward). Sure you'll say that this can be done through bounty, but that is impersonal, non-specific, and anonymous.
Conditional Cease Fire/Surrender.
    This would allows the attacker to devote resources to other conflicts instead of wasting there time finishing a foe that is already good as dead, and allows the defender to rebel at a later time. The terms could include tribute (%income), limited fleet sizes, and/or one way vision pacts each chosen by the aggressor or proposed by the weaker party. (all to deter future rebellion, but terms must be accepted by both parties)
Being able to add ships to allies fleets
    Exactly what it says. still your ships, your supply points, and you can unattach them at any time.
Phase Stabilization Treaty.
    A treaty for making phase stabilization less annoying among close allies.

Random wishes
A superweapon tab: for managing multiple super weapons (similar to the later C&C games where you have a tab for super weapons that will select a super weapon you own till all charged ones are used up, hold shift to select 2 at once)
Multiple sizes of planets of the  same type: This is mainly aesthetic. but population could vary slightly as well
Non suicidal pirates: pirates that don't fight to the death or that move on to other planets.
A pirate cap ship: one can dream, can't they?

This list might be short or pointless, but I tried. Maybe I'll remember more later.