That is a legit concern Rhaw. We are currently exploring ways to make the command more obvious.
Its in the tutorial -- past that, there's not a lot you can do other than going with older, more frequently known, and (frankly) inferior systems. Don't
loose the current system.
That said, the ability to position ships to jump out on command (aka I give the order and they jump THEN, not 30 seconds from then) would be nice. As things stand, the most you can do is order the group of ships to the edge of the system, and tell them to be ready to jump individually -- which can take a while to get them in place, which isn't good when you've got what amounts to a "nodal" response force that needs to jump out when ordered
Just to show you what I mean, imagine a "cluster" off three planets, two connected to the star and
to the third planet -- which leads off towards a plasma storm and the rest of a "space" -- with a very
sharp angle between them and the third planet (as well as the star). With the command, one force could (easily) guard each of the three systems from enemy incursion (be in the "node" system, jump out to either of the sun connected planets).
I actually faced this situation in a recent game -- two planets, whose phase lanes connecting to the star were just a few degrees apart, making it impossible to gauge pirate / enemy attacks destination even with a scout in system until after
they'd actually jumped. The connections to the third planet were further apart, but one fleet placed in between both phase lanes would have been in a perfect position to jump out with only minimal "lining up"... except there was no quick way to get all the units placed right on the edge of the system. Which didn't work too terribly well even manually, seeing as how units all move towards a common jump point even when they're told to jump separately. (Bad, bad move devs!)
Speaking of which, another thing I'd
like to see is having ships calculate jump pathing independently when they're given a move order and are told to jump singly -- as things stand, they'll all head to the same
spot, ignoring what might be quicker for them. Saves a minimal amount of system resources (I think) compared to the annoyance of having to give the jump order ship by ship. (Try having cobalts, say 20 or so, spread evenly around an entire star system to test this, its a good way to see the problem)