Here's a couple design ideas that could have rather big effects. I'd like to hear your view on it:
* Saving throws: Instead of adding a single ability modifier to a save bonus, how about adding the average of two ability modifiers:
Fortitude save = 1d20 + Base Fortitude Save + (Strength modifier + Constitution modifier)/2
Willpower save = 1d20 + Base Willpower Save + (Intelligence modifier + Wisdom modifier)/2
Reflex save = 1d20 + Base Reflex Save + (Dexterity modifier + Charisma modifier)/2
For the fort and will save it seems quite appropriate, and for the reflex save it is too if we assume that charisma is a reflection of the character's grace and smoothness of movement.
-Advantage: all abilities would be of use to all character classes
-Disadvantage: characters would be less likely to have very high or very low saves.
* Armor Check Penalty on Reflex Saves: a character in armour would suffer a penalty to his reflex saves equal to the armour's ACP.
The ACP could be tweaked to go from 0 to 6 and there could be two 'Armor Reflex' feats, one to cut the penalty on reflex by 50% and the other to cut it by 100%.
-Advantage: it would make sense as it's harder to move in heavy armor, it gives more meaning to the ACP, it promotes the idea that full plate is not always better and it helps differentiate between the various armour types.
-Disadvantage: a character in heavy armour and without the appropriate feats would be very likely to take full damage from a fireball.