At first I really liked the idea of +3 to all class skills. But after making a fighter, Bard, and a Rogue of 1st, 5th, and 10th level; The skill "points" all came out much higher than in 3.5 after 3rd level.
So I thought about the idea of Favored Skills. you gain +3 to all favored skills. you would start with 2 to 4 (maybe 6) Favored skills (depending on class) and would gain 1 more at 3rd level and every 3 levels (3rd, 6th, 9th, etc.)
this would slow down the (in my opinion) overpowered skills, and focus your character on what role he or she is trying to be.
just an idea :)