I'd really like to see them get some sort of bonus back, even if it's small.
I realize there may be solid choices to make them an investment, but they feel TERRIBLE when you need a skill, and must wait three to five levels for that skill with almost no benefit until then (see Loadout Design level 3, if you have no Technology. You may say "You don't NEED that skill, though", and maybe you're correct, but having recently just tried it... it makes everything more fun.)
As a side note, practice does make you better at things. Sure, hurting yourself on a fire trap and then healing the resulting burn is a bit silly, but it would work. Do it often enough and you'll learn lots of things. Firstly, how fire traps work, how much they hurt, how to set one off when you want and not set one off when you don't want, and also, lots about how you heal burns, how long it takes, how much it hurts in the meantime... It's a silly example, yes, but it's also a perfectly viable example for how people actually learn. A well implemented version of this for aptitudes, as suggested upthread, would be pretty fun I think. It might indeed be nothing like Alex wants or wishes to design for and that's fine, I don't need or expect him to produce it (oooh, mod potential there!) but I think it would work.
Ideally a bonus orthogonal to the concrete skill benefits, such as dialog trees or specialist market knowledge or something else like that would fit great, but if that is indeed too much of a stretch to actually come up with all of those, just some low grade benefits spread across the whole aptitude would be nice in my opinion too. Even if it's only like +1% hull per rank or +1% ECM per aptitude (total, not per ship), bonuses that do something would really help the -feel- of dead levels. If you keep them low enough you'll never pick them up JUST for the bonus, but it'll really change the psychological effect of buying one, for the better, in my opinion.