I've had this thought too. A mere 1% per level isn't even close to worth all that clicking to level a skill even close to 100.
Like you said, the only ones that are potentially worth it are the ones that give job success chance and the one that gives co-worker affection because for some reason, the co-worker affection skill gives 3% per level instead of 1%.
My reasoning was that the primary use of skills was applying for better jobs & improving your job performance. The upgrades were just supposed to be a small side bonus.
But I've been thinking this over and I think I'll buff these upgrades to make them more rewarding. I'll also reduce the skill XP requirements for levelling them (this will be retroactive so your work won't be wasted).