So, what is your strategy regarding reputation? Are you more likely to snipe particular reputations that are of use to a character, or are you likely to do all of the reps for a given character? Do you expect your strategy will change when we get tier 6 reps?
I have rather too many characters but so far I have completed all the reps except Gamma. My strategy is to finish rep on one character that won't acquire too many items and use them to sponsor all the others. Ironically it was my Jem'Hadar that I used for Gamma. While I am finishing those 40 days, I acquire my 625 marks for all the other characters, by whatever combination of Recruit rewards and queues may be necessary. Once I have the sponsorships, I map out what items I want to get with each character, figure out how many marks are necessary, and do a queue in that rep once per day with as many characters as I can bother doing. Everyone gets at least one item for each rep for everyone who wasn't specifically getting a set. By 20 days I generally have enough marks to get whatever I had planned. Once I have all the items I want, I zero out my marks for dilithium, and keep it zeroed.
Obviously, me zeroing my marks was stupid. I expect I will choose one rep with each character to acquire whatever items tier 6 allows, and level up just that one. I really hope they have some kind of hassle mitigation like another Recruit event.