Playing around with a spreadsheet I made, it seems that the idea of having the 1+1d6 for the number of movement points seems a bit random, but otherwise appropriate, it provides enough of a correction variable to remove questions about order delays, time at maximum warp and other stuff.
Thinking about it further:
Their needs to be at least three modifiers:
Squadron Speed: ships with cruise warp speed of 3.5 to 5.5 shouldn’t get a modifier. 6 to 7 should get a +1 modifier and above 7 should get a +2 modifier.
Mission: a ships mission should really effect how far it can move.
Admirals: as you noted if you include admirals in the game, they should be able to give advantages in how far their fleets can move. This could further be modified by the command facilities and any scouts attached.
Not a modifier, but an option, a fleet should be able to declare if they want to go for maximum warp on a turn. This would double the result of the die roll (so a fast squadron (+1) would get 2+(2x1d6) or a maximum of 14 movement points), but if it rolled one and then rolled one again, it would have to take some penalty and likely cripple a ship.
Like in Fed and Empire you could have the starbases ,outposts planets and shipyads printed on the map for less counter use . The counters themselves could be double printed on one side the up sode is the group it belongs too Federation Klingons and such pluss its size Fleet,task force et cetera however on the back is its combat pool and in some cases it could be a dummy counter to fool enemy forces .Only time you reveal the underside would be when you engage the enemy or they sucessfully scan the counter. Got the idea from the old Hunt for Red October board game