Yes, I "borrowed" this from someone, but, I think he worded it well:
Klingons do not have science ships, meaning they are comparatively helpless in detecting cloaked ships. This is the biggest and most important reason.
Not only is MES a superior cloak, its easy to get. Any newbie science ensign right out of Starfleet Acadamy can cloak a Galaxy class cruiser better than Klingons can cloak a Bird of Prey (I mean come on), and
Klingons can't counter it like Federation science ships. Burning the various detection skills with long cooldowns is not a very good alternative either.
Cloaking and MES are entirely redundant skills on Klingon ships except for birds of prey with battle cloak. If I am in a raptor, battle cruiser, or the carrier, I can use either cloak, or MES, not both. If I de-cloak and attack, I can't recloak early using MES, and vice versa. If you take MES as a Klingon (non-BoP), its as if you just threw your cloak skill into the toilet and flushed because no you cannot use them both. And you still can't detect a cloaked Federation ship.
It is only slightly better as a BOP because it means if you need to recloak <20s after you decloaked, you can. If you can regularly survive that long then its just redundant.
The other advantages MES gets are all bugs as far as I'm concerned, and should be fixed. Shields are a giant floodlight as far as an energy signature goes, and need to be disabled with this skill. Capturing points and laying mines with MES are clear bugs too.
But the skill itself needs tweaking because Klingons can't counter it like Feds can, and it is entirely redundant (once the bugs get fixed) to most Klingon ships.