A couple of examples to see how this would work:
Take the Altmer.
Currently they have a + 10 in ilusion and +5 in the other magic schools and enchanting.
With this mod they would have:
a 20% reduction when casting ilusion spells
a 10% reduction when casting spells from the other schools
their enchantments would be 5% more powerful.
Take now the Nords.
Currently they have a + 10 in two-handed and +5 one-handed, block, light armor, speech and smithing.
With this mod they would have:
a 20% reduction in stamina when performing powerattacks with two-handed weapons
a 10% reduction in stamina when performing powerattacks with one-handed weapons
10% more effective blocking
10% more prottective lightarmor
10% better prices when bartering
10% more powerful armors and weapons when smithing.
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I didn't play the game enough to know if these percentages (20%, 10%) are too high, too low or just right so they may be changed. Still, I've been pointed out that there are pretty large percentual reductions/increases in the game already (like 50% frost resistance and the like). Therefore, and since the idea is to create skill bonuses that do matter in the long run, I think I shouldn't go lower than 20% for the big bonus and 10% for the minor ones.
Thoughts on this idea?

. I was going to do same but on a much more limited basis, i.e. just create a custom class foe my characters.