Apart from rare traits like Efficient, what's so great about non-common BoFFs?
With regard to the original poster:
Think of it this way: Starfleet Merits represent an ability to pull strings and call in favors among the fleet's brass.
Whenever you train an officer, whether through a skills trainer, or personally, they're spending time learning a brand new skill or procedure to replace some thing that they already knew. That means they/you are not doing other duties, and that requires some lenience or special dispensation from star fleet, which is why it costs you merits.
I've never been an officer in star fleet, but I have been an NCO in the Marine Corps. Whenever I wanted to train some one in my platoon in an area that wasn't part of their core responsibilities, I usually had to justify that to my CO, because that was one less body that was available for whatever, and in some cases it meant pulling in a third party to help them learn. Although we trained constantly, there was only so much room to put a personal touch on things. Most training was done as a unit and by the book, or through established channels like Corporal's Course or Rifle Certification.
Getting people into specialized training like Spotter School or NBC School often meant playing politics, because there are limited seats, limited ability to let people leave the unit for training, and lots of need for that training. I never had a "currency" like "Starfleet Merits" that I had to spend, but my ability to get people (including myself) into any special training often relied on the high opinion of my CO or regard that his superior officers had for him.
So you can look at it that way, or you can just look at it as "That's the way that merits are designed to work, so just deal with it." Either way works.
And a g a i n... If it were Starfleet training them (ie me sending them to ANOC or the War College) then sure... I gotta pull strings or whatever.. thats what merits are for. But its not, its ME skilling something to level 9 and dragging my BO into the holodeck or simulator or engineering room... I'm the one doing the training not Starfleet. Its all in the source of the training.
As far as "That's the way that merits are designed to work, so just deal with it." Uh... no.
I dont think thats how its designed to work. I think that I'm dealing with a software engineer that decided to re-use some code. Only when they added the code for captains to skill BO's they used the skilltrainer code from the Starbase Trainer, which charges merits, instead of using the code that Bridge Officers use when they train each other; and subsequently does not.