The first request is the ability to set a rally point PATH. My navy had taken a pounding and needed to be built up again, so I set my production planets to work. There were two routes to get to where my navy was, both of which were of nearly the same length. I assigned the rally point, and went on my way.
I was getting some alerts of 'reinforcements have joined the fight' so I went to where it was calling me. The wormhole, which was lightly guarded by a detail of carriers, was also the route my little ships were going - one at a time. There was a massive glut of enemies built up where they'd jump to get to the next system, and they'd destroy one, while another would blindly charge over to the edge to get ready to jump again, only to be exploded.
Needless to say I was a little miffed that instead of going through the SAFE systems, the Rally Point sent them through uncontrolled space.
The second feature I'd like is the ability to set 'fleet makeup'. So I can say "I want this fleet to always have 10x Flak Frigates, 12x Siege Frigates, and 30x Attack Frigates". Whenever one is destroyed, the nearest non-occupied production planet will build a replacement and send it off to join the fleet.
Honestly, that'd save me a TON of asspain, especially since fleets sometimes have a habit of 'losing' fleet members.