A thought that I have tested with my friends is can every skill have a synergy, and can feets improve with skills. In practice this has work quite well here are some examples:
For every 5 ranks in... You gain +1 to (or the old when you have 5 you get +2)
Acrobatics: Climb
Appraise: 5% haggle bonus for prices (so not really +1 anywhere)
Climb: Grapple checks vs creatures larger than you
Craft: Varies on which on you have (ie craft (carpetry) gives you bonus on knowledge (engineering) for wooden structures)
Deception: Disguise checks
Diplomacy: Leadership score
Disable Device: Knowledge (engineering)
Disguise: Stealth
Escape Artist: resisting grapple checks
Fly: Acrobatics
Handle Animal: Ride
Heal: Healing spells and abilities are treated as one level higher
Intimidate: DCs for fear effects increase by one
Knowledge (arcana): Spellcraft
Knowledge (dungeoneering): Disable Device
Knowledge (engineering): Craft checks
Knowledge (history): Appraise vs old objects
Knowledge (local): Survival checks made in that area
Knowledge (nature): Handle Animal
Knowledge (nobility): Diplomacy
Knowledge (planes): summon spells are treated 1 level higher
Knowledge (religion): Turning level increases by 1
Linguistics: Knowledge (history)
Perception: Iniatitive
Perform: varies on which on you have (ie preform (oratory) give you diplomacy)
Profession: Also varies from which one you have(ie profession (teamster) you are treated one level higher for carrying capacity)
Ride: Acrobatics
Spellcraft: +1 spell penetration
Stealth: Theft
Survival: Knowledge (nature)
Swim: swim 5ft faster
Theft: Deception
Use Magic Device: this skill should be combined with spellcraft
If there is any intrest I can post a complete list for craft, perform, and profession later. The really goal of this is for characters to be reward for working on skills, as in the CN rogue will get really good and what he does by taking a group of skills that compliment eachother. This can go even further, to make feats that as suppose to not be good at all be very good at later levels with alittle planning.
Example: Dodge, feat stays exactly the same but add that for every 5 ranks of Acrobatics you have the AC bonus increases by 1.
OR
Favored Enemy class ability: for every 5 ranks you have in a knowledge relating to your favored enemy you gain a +1 vs them (yes a reason to take knowledge (dungeoneering)).
This will make dodge good at low levels and worth keeping in high levels by level 17 the bonus is +5 vs a single target making it valued and not just a preq for whirlwind and spring attack. If there is further intrest I will dust off my old notes and give you a more complete list of altered feats.