Wasn't there an optional rule in Hero System's supplement, Ultimate Skill, about lessening skills that you don't use? I don't have the book myself, and do not recall using the rule in any of the games I played in, but I remember thinking it was really cool.
I see the concept of skills degrading from lack of use pop up in RPGs very seldom. It serves little useful storytelling or strategic purpose.
There are some games that offer a benefit from lowering a skill. You already mentioned FATE that lets you increase a skill by lowering another if the two skills are one point in difference. There is the almost unknown Destiny System that will award a player sand points (a measure of how interesting and thus likely to survive your character is) for declaring weaknesses for your character. Thus if you can't remember a spell that would make the adventure a lot easier because you haven't cast it in ages, or if you can no longer hold a calligraphy brush properly because of a scar on your hand, you get 2d6 sand for each of those.
There are games with aging rolls, but those usually lower attributes. They are more common than use-it-or-lose-it systems because you can say your character practiced unused skills in down time, but you can't say your character didn't age. Plus a character that looses some proficiency as he gets older does add something more interesting to the story.
I recall a really nicely conceived amateur game from a few years ago that forced characters to make aging rolls every winter (past a certain point) and lose points off their traits (which were kind of skill-like, in that there were 16 of them, and Craft and Sneakiness were traits). And... hooray, I still have the link for it. Dark Age
Then of course there's Rolemaster and games of that ilk (games with horrible critical injury charts). Characters have to have access to magical healing or a single critical injury, "Slash muscle and tendons in foe's lower leg" can put a serious damper on his future as a track star. That's not skill atrophy from lack of use but from disabling injuries. This is also more common than use-it-or-lose-it, because it serves that tactical and narrative purpose of making players seriously weigh their options when going into a fight.
I would argue that skill loss from illness and injury is even more realistic than just forgetting because you haven't done it in a while. People who haven't spoken a language in years may say they've forgotten it, but if they were dropped into that country they would remember a lot faster than someone who never knew it. But a singer could get a respiratory illness that ruins her voice. A musician could get a scar on his mouth that prevents him from playing the trumpet. Let's not even think about the fact that most people who are shot never fully recover.
One source of skill loss that I haven't seen and would really love to, is a cyberpunk game that lessens PCs' technology and social skills unless players constantly invest at least a little in their advancement, a kind of Red Queen's Race situation where if they don't work to stay abreast of the latest fashions and technology, they will be left behind.