What I think of when see a skilled called Mask energy signiture is a ship lowering it's power levels to reduce chance that an enemy will detect you. I'm not talking cloak in any form.
What I think should be done is make MES a active 30 sec stealth that will make you invisible up to 15 km sphere around your ship but all your energy levels will be lowered to 25 power and you will not recieve power bonuses (kindof like when your using full impulse) while MES'd. Once an enemy move within 15 km of you the stealth will disappear, if you enter combat the effect will end, or if you activate an ability other then full impulse or shield distribution the effect will end. Higher ranks should increase the maximum power levels you can have so MES 3 would allow you to have 50 power across the board. Also MES cannot be actived while in combat and can only be activated out of combat.
I think this would make MES more useful then it is now and allow ships that don't have cloak to be stealhy without all the benifits of cloak since you can't do any actions other then manuvering your ship. The 15 km detection range should make the skill less useful then cloak with you can get within 3 km of most ships without getting detected.
The problem with that is that it doesn't become useful enough to warrant a BO slot. Your idea would make it weaker than it is in PvE currently, and mediocore at best in PvP. Klingons get an effective Cloak without having to use up a BO slot, slot consoles, or spend skill points to make it effective. Feds do not get that luxury with MES. The fact we have to slot MES, stack consoles, and spend skill points to make it effective should be enough of a crutch to get the effectiveness of Cloak (again, MES is used out of combat, so we'll never have a Battle Cloak). MES 3 with appropriate stat stacking (skil points, consoles) should be the effectiveness of Cloak. Sit up right next to your target. We already suffer the power penalty which causes a delay before we can start firing after breaking out of MES. MES 2 should have 75% effectiveness with stat buffing. Get within 8km of your target before having increased stealth loss. MES 1 should be 50% effectiveness, probably about 12km.