@SCC: It'll warn you if you have help popups enabled, though.
That said, I kind of like the idea of an aptitude providing a small bonus based on the skill points spent - but it's not clear what that should be in every case. Combat is the easy one, but other aptitudes have applications on several game layers, so there really isn't a fully-representative effect. It's just a lot cleaner to only have them unlock new skill levels.
You could add a bonus to each skill based on the level of the corresponding aptitude, capped by the level of the skill. So, take Surveying for example. The Skill Bonus increase the difficulty of Planets that can be surveyed and unlock surveying equipment as it does now, but in addition, each level of industry could give, for example -5% (rough example) crew/machinery/supplies needed to survey, capped by your level in Surveying, so Industry 3, Surveying 1 = 5% bonus; Industry 2, Surveying 3 = 10% bonus etc. That would allow someone to unlock the ability to survey for 3 points, but someone who was focused on industry, would be
Better at Surveying and could do it more efficiently. From the UI perspective, that could be in the skill description portion of each skill. It would require coming up with what the Main value of the skill and what the Aptitude value of the skill should be, but I think for most skills, I don't think that would be too difficult.