I'm thinking that 1.04 will be small changes, balances, and 1.1 will be the big overhaul, so that leaves out sweeping diplomacy / black market changes. I'd like:
Ability to shift-click a research item to start it researching immediately (any item currently being researched on that sheet pauses, then resumes after).
In another thread someone was asking about Homeworld style ctrl-drag selecting targets to be attacked, where your ships would try and kill those targets before targetting anything else (i.e. focus-fire on a group of ships rather than an individual). This would be good, but I think it'd work easier without the clunky drag mechanic; It'd be nice if you could switch to the stacked view in the empire tree and right click an enemy stack (currently this makes your units just attack one ship from that stack and then go back to auto-targetting).
Another button in the search panel for normal ships (or 2; Frigates and Cruisers), which would expand to allow you to select individual ship types. It'd also be nice to have a text box you could type into to search for named objects like planets (yeah, my allies don't know how the ping function works).
Returning Armada obeying the rally point which has been set for the planet the phase gates orbit.
Ships auto-targetting; higher priority should be given to ships in front of the ships guns / inside weapon range. If the ship has been told to hold position or is in fact incapable of movement then it should always target ships inside it's range over ships outwith.
Ability to toggle the flip/flop abilities per group rather than having to tab though each ship (assailant ability being a prime example). Assailant ability (and others like it) need better autocasting; if I tell my ships to move when they are in siege mode and the ability autocast is on then it should bloody well instantly cast.
Should be allowed to fire my kostura cannons at planets where my allies have fleets. If I can accidentally nuke myself then I should be able to "accidentally" nuke them too

More importantly, I can't even fire it when they have a small scouting force there (which would let us see the pretty explosion).