Some of these ideas are mine others are from other players, given the large amount of discussion on the Reputation system it is impossible for me to remember the names of those players. Right now I see only four options available, with one must upgrade.
1. Reducing all lock out timers to no more then a 24 hour time period.
2. Removing all lock out timers, but increasing the cost of omaga marks for each mission drastically to a point that is somewhere in between extreme and casual. Possible issues with this is it would difficult to pick the right number of cost for each mission.
3. Removing the Reputation system from stfs and putting in the old system. Honestly at this point if the devs were going to take option three, they would have done so by now. Or atleast made a announcement that they were taking this route.
4. Keeping it the way it is, given the fact that I have met no one who likes this system in its current form, this would kill star trek online. It can not remain the way it is.
Now on the upgrade part ive seen a few posters suggest this and I think they are right on. There needs to be a added mission slot to the mission slots for the upgrade, once you get enough rep for a specific tier. To build upon this idea. I also believe two more mission slots should be added for unlocking gear. The reason behind my thought on this is, this way somone can conintue to progress to the next tier, while continuing to do missions for gear they want for themselves. Given the cost in omega marks, I think it would be safe to say it would give everyone a reason to do stfs again. Instead of sitting on there arse.
My thoughts on this are simple take option one. Add 3 new mission slots, one for upgrade, and two for gear. Reduce gear unlcoks to a 60 minute time frame. Now the thought behind this is yes the unlocks would be greatly reduced but even going full speed on the set up I have just proposed, they will have to stop and do a great deal of stfs to come up with the omega marks required. As gear cost via omega marks is not cheap.
One of my biggest gripes with the current system is I am mortal, meaning I am no longer young. Hopefully soon ill be at a point where I wont be able to play sto that much or at all. The way the system is set up it is a constant reminder of how much time has gone by, and how much more time you have wait to go by. This is just dang depressing. This is why I favor a 24 time frame over the current time frames.
Developers I have voiced my opinions on this system in many posts, but I truly hope you give this post of mine a hard look. As sto is one of the few remaining mmos out there with some substance and potential. Most importantly I am a Star Trek fan, but not a fan of JJ Adams Trek.