Plus and minus signs having that wonderful time dialation function would be a real big help. Over all though, the game is just abysmally boring inbetween combats.
It takes a long time to get started, something alleviated by playing a flagship game, but even with your economy rolling along it's a very lengthy game. I actually watched a movie while I cleaned out the second solar system in a 10 and 2 custom game. The ai being unable to kill capital ships made it a little more boring than it should have been, but transit times are just plain lethal.
The pace of combat is great, aside from speed variation between the classes I've got no problem with the in gravity well pace of things. Jump charging delays are a neccessary thing to keep people from just warping in and out with impunity, so I'm not suggesting you get rid of those either.
I am suggesting that jump transit times be butchered though. Particularly between systems, the gravity well of stars could use some help too. They crawl along at an ungodly slow pace, it's a good time to eat or something. I often build defenses to kill invasions after I see them jump in system as well, they just don't need to be so long. Any movement of forces from other systems will have the same delay, duration is only important for how long it takes you to notice and find the invasion point. Giving you time to get things moving is one thing, but it's so drawn out that it just plain kills the game for me. If there were tons of stuff to manage, like beyond civ's level of management, maybe I'd have something to do while I waited five minutes for this and five minutes for that, but there's just nothing to do while you watch your fleet crawl across the map.
My next game I'm going to try spidering my approach and just building fleets for every new target and scrapping the old ones, I'm pretty sure it will go faster.