Going through the skills section of Pathfinder made me think.
Why not take a leaf out of Mechwarrior?
Skills were bunched into oblivion in 4e but the reason, ease of starting a character was valid. The lack of skills for task resolution rather than just combat resolution was also just as valid.
In mechwarrior, you get skills and subskills. Lets say technician as the skill but also subskills like technician/engine, technician/sensors etch. mechwarrior's way of handling would be to allow you to get a +1 bonus at a cost of -1 penalty to all other subskills, but thats not really good enough IMO.
If the skills were grouped BUT subskills were also available, you would have 2 levels of complexity. For DMs who wanted to play fast and easy, they would ignore subskills, using only the group skills. For groups who prefer realistic or like complexity, they could use the subskills.
Take for example atheletics as a main skill with jumping, swimming climbling as its subskills.
Atheletics 10
Jumping 10+5 competence
Swimming 1
Climbling 10 +4 competence
To prevent skill ranking from going out of whack, reduction in a subskill for specialization in another subskill would be a competence bonus (which overrides many magic/item effects)
For novices, they could simply use Atheletics and the equivalent of having all the subskills at 10