Reputation passives, activated abilities, and equipment are all necessary for high-end gameplay. Leveling those reputations costs players nothing but time (as the only limiting factor is marks). But that time is not only gated by the number of daily runs needed to get the marks (unless you happen to be able to play specifically during the bonus mark event every day), but also by a 20 hour forced wait between projects as well.
As such, completing all three reputations to full on one character can be rewarding. However, once finished, being faced with the daunting task of doing it again on another character is a complete deterrent.
The release of the new Romulan Scimitar Dreadnaught pack made me realize this recently. I like the ship. I want the ship. I'm willing to purchase and pay 5000 zen for the ship, as well as the hundreds of thousands of dilithium needed to outfit it.... But I'm not willing to spend 4 hours each day grinding for the next 2-3 months to get the reputation needed to equip the ship.
The part I don't understand is... Cryptic should want to make money. We want Cryptic to make money as well, so the game can stay alive and active as long as possible. Cryptic makes their money off of Zen and Dilithium, neither of which is needed UNTIL AFTER the reputation system is completed (as space equipment costs a lot of dilithium, but nothing while leveling the reputation requires any).
So here I sit, as do many others.... with a Klingon... with a Romulan... with other Federation characters... with a wishlist of things to purchase using dilithium and Zen, with the only thing standing in my way of purchasing them in the form of a huge time sink.
I did it with one character. I won't do it again. And I can't help but wonder why an account-based reputation system isn't in place yet. Each player will still need to run STF's and other PvE activities to get the marks to purchase the items they need, and plenty of times.
There's money that people want to spend... money for Cryptic to make... if they'd just let us do it without all the frustration. Doing reputation once is enough.