Yeah, that really irritates me too...
the biggest thing is when fleets simply dont jump together... ill have a large fleet massing to jump, and my lone Akkan will grow balls all of a sudden and go flying into battle, while the rest of the fleet is still waiting for the slow as f*** Assault Cruisers to line up, and then, when the rest of the fleet jumps, my Marza and a handful of ships are still left at the previous GW...
i also get fleets splitting up, running through milita or enemy controlled worlds, forcing me to rebuild the losses it take... Scouts dont scout, they sit there... or run for pirate bases or the worst possible route... fighters and bombers always find the worst place to sit.. either right on top of critical structures, or on the opposite side of the GW from where the bad guys are coming from.
and i dont even use the Empire Tree, just because of the jumping thing (well, its also because im using 1920x1200 resolution and the icons are so small its easier to find ships by 'tabbing' through the fleet)
another thing actually, auto-pinning Starbases, without the option to turn auto-pin off, is really annoying. ill build a bunch of starbases, and find all of a sudden my empire tree looks like Stalingrad during WW2... having had the flying f*** bombed out of it... one time my ET had scrolled to the bottom for some silly reason, and i freaked out because i thought one of my fleets had been destroyed and i didnt even know (i was playing with the sound muted)
honestly, it isnt that important to see which ships are in phase space at any given moment... most phase jumps are so quick by the time you need something, or finally found something, its already over. its only barely useful for Vasari, because they'll be able to tell when large numbers of enemy forces are moving anywhere on the map... but for Advent and especially TEC, I DONT CARE!!
lots of things are screwed up with fleet manouvering etc... i think IC needs to sit down and have a long hard look at it.