I propose that you add more "contested" planets. in groupings of 4-10, each requiring a mission chain of medium length (100-200K energy), and a single legion would be required to invade and hold atleast 2 or 3 before seeing any bonuses.
There would be many chains, think of the planets as belonging to a solar system, im thinking 10 or more systems with 3-8 planets per chain(system).
bonuses could be a simple 1% increase to base production per planet (but requiring atleast 2 or 3 be held before seeing any bonus) and only one planet could be held per legion member. also you would be ineligible to steal planets of a different system(not sure how hard that would be to code, maybe something simple like when a legion gains 3 planets of any system, the legion itself gets a denomination and would restrict any other thefts of different systems.

Other bonuses could be extra base attack, defense, hull, even legion bonus for planets, an extra 5 or 10% boost to cloak would be awesome.
Possibly an increase to the players attacks as well.

Not sure where the mission chains would fit into things, but i dont think releasing them as dailies would work, but rather just dumping them into the missions list would be best, that way a legion would have to work together towards goal X as a whole.