the reputation system is definately a step up from the random luck method of the old days (still the old old days were the best, with 1 run for 1 set piece)
i see 2 major flawes with the reputation system...
1.) it allows to grind a single mission for each reputation faction (the most efficent), which gives opportunity for for lazyness: i liked the old way where, if you wanted MKXII ground items you had to do ground combat...the only real dumb part was the insanely low drop rate, 1-3 runs should be sufficent, period.
2.) it is very alt unfriendly
my 2 possible solutions: token drops for each different type of set item and mission (was already in the game)...which are tradeable, and are needed to start the set item projects. For lower than MKXI, you don't need those drops...for MKXII you need more than 2 or 3 of a certain type. Similar to the omega drop that is in place now, but each stf droping adifferent kind, so that players are forced to do all stfs atleast once or twice. Anybody who still prefers, or finds certain content too hard can buy it from the exchange, or trade it from a friend or fleetbank.
for instance: the nukara ground set needs a specific item that drops in one of the two elite ground missions with a 30% drop chance. Space items need a drop either from elite CE, vault ensnared or azura nebula.
Romulan space sets could be a reward for doing specific dailys on new romulus, or some of the new missions that went life with LoR...or 1 new stf/CE like mission that awards 40-60 romulan marks (the broken tholian-borg event comes to mind, this could be a fixed and queueable event)
and second: all gear from the reputation should be account bound...and all marks gathered (including fleet marks) should be account wide.
cryptic want's you, the player, to spend dilithium on items...the old system didn't do that, thats why it is gone forever.