One of the things that bugs me the most about Star Trek: Online is a completely lack of complication in the way that systems onboard a ship work. Do not get me wrong, the game is good and I am enjoying myself much more now then I was (partially because I stopped playing it more often and gone down to a couple of hours each night)
However I have a suggestion,
Every shield the game should have a number attached to it. This number is the "shield frequency" and helps bolster the resistance of the shield. This number can also be exploited if another player manages to match shield frequency and then can make kinetic damage pass right through shields.
This opens up a whole new world of tactical gameplay in which an Engineering Boff level ability can be gained called
"Randomize Shield Harmonics" which effectively allows you to change that base shield number and would be essential in Borg STF's to prevent the Borg from penetrating your shields.
This can also be tied into science in a way that they can do deep invasive scans and uncover a range of possible shield harmonics which they can adjust their weapons to during a fight.
Beams could also have their "frequency" shifted via a tactical ability to do 100% damage through shields with a frequency match in the same way that a BoP was able to take on the Enterprise-D until the other player either "resets" or "randomises" shield harmonics.
These concepts are seen in multiple different Star Trek Episodes.
Like I said, this is a rough idea to bring a more Star Trek element into the game. Please do not just say things like "this is terrible" or "this would never work in game" but please try to provide constructive ideas and criticisms. If you do not care for the idea, please state the reasons WHY you do not care for it.