Just some quick brainstorming on how to add debuffs to the current scoring system. Some kind of system is basically required before any kind of universal ranking system becomes feasible, and no offense to Cryptic, but the fact that they themselves don't seriously PvP means that any system they come up with on their own will most likely be heavily flawed. So this thread exists to try and help guide them as to how such a system should be designed.
What makes most sense for many skills is a system where we use the equation (and for debuffs that effect many targets this can be used on a per player, with NPCs *not* counting, basis):
(strength of debuff) * (value of specific debuff) * (time that debuff is active) = points

Strength of debuff is self explanatory. A tyken's rift that drains a small amount of power counts less than one that drains a major amount of power.
Value of specific debuff is not so selfexplanatory. Basically, some debuffs are worse than others and should be counted that way. Jam sensors should give a very small amount of points because it does not make a very big difference in the overall scheme of things for a battle (and is also a very low level skill). Scramble sensors or gravity well on the other hand, can make a huge amount of difference in a battle, and are both higher level skills. They should give more points when used and thus should have a higher value here.
Time that debuff is active: Also self explanatory. Every second a debuff is active (or in some cases, every 'tick' of the debuff) should give more points. The debuff continues to accumulate points until it is cleared or runs its course.
Now, this method is great for some skills, but is not great for all of them. Here is a list of debuffs and how I think would be best to score them:
Gravity well: Formula above. Given a high value. Could possibly merge strength and duration since the two tend to be related and strength gives a bonus to damage score anyway.
Tyken's Rift: Formula above. Given a high value.
Jam Sensors: Formula above.
Scramble Sensors: Uses formula above with duration and power combined as one value since they are one and the same.
MES: Tricky. Cannot use the formula above. Needs to give points whenever it lets the user go undetected against someone who would normally see them. Cannot give points out of combat or it will be abused. This sounds a bit unfair but is not since effective use of MES will help the user get more points in kill/death/damage/healing anyway.
Energy Siphon: Uses the formula above. Given a higher value when the use of energy siphon contributes to taking a subsystem offline.
Viral Matrix: Uses the formula above (for each of the four specific debuffs). Can merge power and duration since they are the same.
Tractor beam: Uses the formula above without a strength modifier since the strength only effects kinetic damage which is counted in the damage score.
Tractor Repulsors: Uses the formula above, with 'time active' in this instance starting at 0 and incrementing for every successful tick. Strength determined by the distance repulsed and not by kinetic damage done.
Polarize hull/APO: Gives a moderate set amount of points when used to clear a tractor beam and a very small value for every tick that a kinetic knock back is averted.
Tachyon beam: Uses the formula above, given a small value.
APB/APB/FOMM/SS: Any extra damage that is a result of the resistance degradation gets added to the user's debuff score. In the case of sensor scan, revealing cloaked targets gives a bonus.
Charged particle burst: Does not use the above formula. A fraction of the damage done to shields is added to the debuff score. Any cloaked ships revealed give a bonus.
Photonic shockwave: Gives a small bonus for every player successfully stunned. Does not need a large bonus since effective use of this skill will increase kills/death/damage/healing scores anyway. Cloaked ships revealed give a bonus.
Eject warp plasma: Uses the formula above. Any cloaked ships revealed gives a bonus.
EPS: Uses the formula above.
SNB: Uses the formula above as well as a small bonus for every ability that gets cleared from the target.
Beam target susbsystems: This is the most interesting one. You can do it two ways depending on how in depth you want to go:
1. The lazy ass way  Use the formula above. Give a bonus if the skill contributes to taking down a subsystem. Not the best way to count things. Draining aux on a dedicated DD isn't effective. Neither is draining weapons power on a dedicated healer, so they should not give many, if any points.
2. The right way  Actually give score based on what the drain does during it's duration.
For weapons  the difference between the drained damage and regular damage is added to the user. You could either make this just hull damage averted, or a fraction of all damage done out of the muzzle (because of the way STO scores  or doesn't  shield damage vs. hull damage)
For shields  the amount of shield regeneration taken away by the drain, perhaps as well as the damage (or a fraction thereof) that is no longer resisted due to the drain.
For engines  In this case the above formula actually works
For Aux  The difference in healing for any skills effected by Aux power is added to the user's debuff skill.
And of course, there is still a bonus for taking any subsystem offline. Perhaps with shields being given a higher bonus for obvious reasons.
So there you have it. Not sure if I missed anything (feel free to add anything that has been missed, or just voice your opinion on what I've come up with), but it feels pretty complete. Also for any Cryptic employee reading this might seem a bit daunting to implement, but a system for counting nondamage/healing skills will eventually be needed for PvP to move forward.