You don't get promoted for being excellent at your job if it's your job is to be excellent. They promote you if they think you can do "more" because it should be impossible for you to do better, otherwise you'd be dismissed.
Kim was excellent at following orders, but promotion from his current position meant that he would have to give more orders and take less. The higher up he goes the more freethinking he would have to be in his ability to make the crew follow his will. Just because Kim could change the ships sparkplugs it doesn't mean that could organize 80 crewmen to simultaneously carry on a lexicon of activities across a broad spectrum of responsibilities aboard ship frictionlessly.
What about the guys and dolls in Security with no engineering background who excel in their profession? Are they never going to be promoted because they don't know how to change the sparkplugs? or are they going to be promoted because Tuvok thinks that can Guard more important doors and sneer more panoramically?
(Can nurse become an admiral or a general if they're really good at their job? I'm sure doctor can. But if you're good at your job, no matter what your job is, surely there's room for advancement... I always wanted to see Hotlips in charge of the 4077th. She was career military, it seems weird that Frank outranked her.)
They handled this on Battlestar quite well. There was a deck hand technician who wanted to be a pilot, and she had almost qualified before civilization fell, but "now" they said that she was too valuable and good at her job repainring ships to be promoted and they couldn't "waste" her sending her off against the Cylon Vanguard if it would take 10 years to train up a replacement for her.
Maybe the reason Kim was never promoted was that he was too awesome?
If they promoted him to management, they'd need 12 guys to replace him, which means that they would have to promote a further 6 Ensigns to Lieutenant to administer all the extra substitute Kim's (all of who would have to be replaced with enlisted personal, who would... and so on and so on...) which would evaporate the lower ranks and (re)place firmly Lieutenant Junior grade at the bottom of the rank totem.