How about planetary problems? You shouldn't be able to just send supplies down on an uninhabited planets (what are the chances) and be able to capture it. And you only ever need one colony frigate. Have a bar that shows the progress of the planet being colonized, have some "resistance" slowing down the bar, or in cases of extreme resistance (planets already owned), have it go backwards. You have to send multiple colony frigates to take down that owned planet (something of the order of 6 to 7) in a reasonable time frame (a minute). Or you could always bomb the hell out of the planet, which would create "resistance" after they have been wiped out because you just destroyed the planet you want to colonize, but is perhaps a third of the initial resistance of a populated planet. Give players the option to persuade the colonized planet to join you, in effect giving you all the upgrades and structures around that planet. A huge price tag (something like 10,000 credits, 2,500 metal, 1,250) to start the persuasion and some full five minutes for it to finish.