It seems the fix to the Enhanced Battle Cloak is not easy. I can only guess why that is so, to be honest, so my fix is also only a guess on what could be faster.
Let's forget for a moment entirely how Enhanced Battle Cloak works.
Instead, let's take Battle Cloak. It has a 15 second cooldown after you decloak, but then you can use it at any time.
Why not create a version of Battle Cloak that has only a 2-3 second cooldown after decloak? And then we call that "Enhanced Battle CLoak" and put it on the B'rel.
The play dynamic would be very different from what we have now, to be sure - you wouldn't be able to just fire a torp or a power at cloak - you need to conciously cloak, use all abilities you want to use, and then cloak again. It will require some more micro-management, essentially, but in exchange the issues of Enhanced Battle Cloak as it is now are gone. As a "drawback" it won't feel like the original version of cloak as people wouldn't just fire torps when decloaking, they could use everything.
Why it might be easier than fixing Enhanced Battle Cloak: It's basically just replacing one number for a cooldown for another. It doesn't require thinking and changing the interaction with dozens of powers and weapons.