I agree that once you hit lvl 50, its STF time for a while. Then you get some cool gear, try Elite, and the PUG nightmare hit you in the face hard. So you try PvP, but its weird and you don't seem to get any good reward from it...
You find out that there are a lot of DOFFs chains in unexplored regions, so you do that for a bit. You join a fleet to have access to more cool stuff, but it turns out that there is not that much stuff you can get from there too.. So you level another toon and the cycle starts over.
OK, so 4 problems here:
1) Once you hit max level, there is not enough "level" of gear for you to get. In WoW, once you get max level, you are nowhere near being geared enough to do Heroic mode or even Raid properly. Your effective power is going to nearly double once you get a proper gear set. In STO, once you are lvl 50, you have access to MkX, XI, an XII. Its obviously not enough. People seem to understand progression by getting new ships, but I am of the opinion that ships should only be a a part of this. Gear progression allows for a longer cycle, and requires less resources from the devs as only Deflector-Shield-Engine need any visuals, the rest is just numbers.
Heck, we could even LEVEL our ship and get, for example, more BOFF slots, more consoles, better stats, etc. Lots of that could even be C-Store stuff that we buy, but a lot could be done with daily quest, assignments and the like.
2) PvP needs its own set of rewards that can be used to balance the PvP part more by adding a new set of variants. It also needs more titles, skins and costumes, trophy, etc. Give me a reason to go learn PvP by being killed repeatedly. I want that pain to matters. Maybe allows people to grind a lot of Dilitium from it, even going over the limit a bit. Make it so that the better you get, the more Dilitium you can refine, etc.
3) Resources. If you want to, you can disregard farming altogether. There is little interest for a player to gather resources as they are not really needed for normal game play, apart from a few DOFF assignment and some Fleet projects.
The gathering process is too long. You get a progression bar, and then you have to play with the sliders, it takes a while to get a single mineral samples. Plus its not obvious to know where what material is. All in all, the crafting side of the game is not engaging. In other MMO, a crafting profession gives you in-game bonuses. Maybe I could be a weapon specialist and get an ACC bonus, or be a Warp specialist and get a Warp Core bonus. Again, its all just numbers, requires no assets in game and give us yet another thing to do.
The funny thing is that there are anomalies everywhere, but at some points you just go Meh, what's the point?
4) Community and Instancing. You know how people always say nobody talk during STF? You know why? Because people have to hold the "D" or "A" key all the time to turn. If you try and type in something, you fly into an explosion or out of range or worst. Give us an "Orbit" function and see how communication increases.
Instancing is a great idea while building a MMO because the architecture is simpler, but in the end, you do not get an open world feel. It also means that there are always barriers to getting somewhere, the dreaded loading screen. Like, why an't I get to Sol System and go directly to ESD or the Academy? Why can't I just GO places instead of going through 3 loading screens just to get to my bank?
The point is that you need to have places and systems that allows and encourage communication. The more people are able to talk, the more tool you give them to create a community, the more "game" you get. Why can't I even inspect another player? How am I supposed to learn what gear to use if I cannot see any examples? How can I learn how do do a STF if the game engine makes it complicated for people to help me out?
This last point is admittedly less about end-game, but I think its part of the problem.
Most of the elements are already in there, they just need a little push and some polishing to make this great game even greater.
A BIG problem is that PvP could be the endgame, and that could cost PWE some players (customers) if they can't maintain the illusion of invincibility they got from PvE, against live players. I think we're being milked for every penny in our pockets, and when lint starts to come out instead of cash the game will get an update- that each toon will suddenly get a grand retirement cutscene, and everyone lives peacefully together in the universe.