So it would look like this:
----------- Misc ----- One handed ----- Two handed ----- Speech ----- etc.
Stealth:
Magic:
Combat:
And the skills would fall under 2 separate categories, as well as attributes?
Partly, first i hate the "big 3" sorting, there is no clear distinction between "this is for class X and this for class Y", so no "all is dividable by 3" and such, I don't even try to squeeze it into that direction.
The skills would be like this:
Skill group:-Subskill 1
-Subskill 2
-Subskill 3...
For example, one group can be "One handed weapons" which for example includes (in my current system) swords, small axes, clubs and hammers (there would be more but i only made 4 for simplicities sake), everything that's "relatively" heavy and large but still wielded in one hand and is a weapon you swing with (ones PRIMARILY used for stabbing [not spears though, they are polearms] are in another group). Every subskill has it's own level so you could have swords at 40, small axes at 20, clubs at 15 and hammers at 5.
However they are also GROUPED which means their levels influence each other, the mechanic behind that is simple, take all levels of the subskills, add them up and divide by the amount of subskills, this gives you the "group level". This is how efficient you can use subskills that are actually below the groups level. With the above example all levels added together are 80, divided by 4 subskills that means the group level is 20, so you could also use clubs and hammers to a maximum efficiency as is they'd be level 20, however you don't actually get the full bonus of actually being at the level out of it. Being experienced with a sword and only having the group skill increasing your efficiency with a hammer means you'll still tire out relatively fast from using you, pretty much you got SOME skills in it already but not as many as if you really trained it.
With this system skills that are lower than the groups level get a little push but not really a level up, sticking to one subskill in a group can make that rise though.
So in total you have a lot more skills you can train and a lot more within that group you can simply use "efficiently". So when your sword gets knocked down a dark hole and all you got it a hammer you're not screwed, you're not as good with it as you'd be with a sword but you still got SOME experience because they handle similarly enough.
The exact calculation could still be overworked, like a skill that is lower does profit a little less from the groups level but this is still open, I just wanted to explain the system in some more detail and hopefully make it a little more understandable.
EDIT: Additionally it has some pros and cons to put skills in a group, the pro is that all skills in the group profit from the group level, the con is that the more are in a group the more the level gets split up between them. A group having 4 skills means those 4 will profit to a bigger degree, one with 6 means more skills profit but to a smaller degree. This kinda balances out how many are on one group, more skills means less bonus, fewer skills means more bonus.
EDIT 2: And on Attributes, each attribute would count towards the subskill it's more fitting to, NOT the skill group. Additionally I'd also change that every subskill can connect into MORE than just one attribute, some weapons require just as much strength as they do speed, some demand more strength, some a mix of strength and dexterity and so on. Which attribute dominates is dependent on the USE of the weapon, swinging a dagger sideways to keep someone off you requires speed, jamming it deep into someones body requires more strength, but they are still ALL needed, the degree of how much just changes.