The other thing is, it's not good for the game if you can do one activity over and over again and get everything you need from it. You will inevitably burn out, and when you burn out, you stop giving PWE money. Since developers stubbornly insist on things like "eating food" and "paying mortgages", that doesn't work out.
That's why an STF can't reward you with massive amounts of gear, Dilithium, Fleet Marks, and rep for a single faction that has all the best gear; it results in everybody just picking the easiest STF and running that all day.
I really, really like the system in WoW, where you can build up your gear through many different grinds of your choice, including combining several, to get your gear up to the point where you can do one raid; which gets your gear up to where you can do the next one. etc. You've always got something different to do, and at most points you can decide "this is boring, I want to go grind some other rep for a while, and get their chest piece". That's where STO has to get.
Since we've already learned of two different faction reps going in (Omega Fleet and some piece of the Romulans), it sounds like they're making a start.