You can make a grind better though by having dynamic missions that change based on the player. The current system involves static missions which do not change at all and some are just downright boring to the point that no-one does them except for the rewards.
I used to play Left 4 Dead and while it only had a handful of maps the game changed and would become more or less forgiving as you progressed based on how you were doing. You can't do that in this game or it would be more difficult but taking an idea from that would be good.
Though I think one thing that would make grind much better would be if all missions rewarded some of the other required marks. This way you could do missions you like and get what you need to plod through the rep system. For example you could play an stf and get 50 omega marks but you would also get 10 romulan and fleet marks. You could play azure nebula rescue and get 50 romulan marks and 10 fleet and omega marks. This way you encourage players to play all the content but you do not force them to.
Also the rep system has the 20 hour timer to make you log in every day. More people logging in daily means it looks like a bigger success and can advertise its wares and tempt you more.