I think the ideal solution is to go with two types of bonuses!
Everything is either an enhancement bonus (which doesn't stack with other enhancement bonuses) or an unnamed bonus (which stacks with everything else, including other unnamed bonuses).
On this view, unnamed bonuses come from abilities that are lasting, important features of the character, like ability scores, feats, and class abilities. (High Strength, the Weapon Specialization feat, and the favored enemy ability would all provide unnamed bonuses to damage rolls.) On the other hand, enhancement bonuses would come from external (or at any rate generally temporary) sources of a character's power--like most buffs and magic items.
The idea would that bonus calculation would be a lot simpler (if it's not basically permanent, just take the highest bonus that applied) and would help reduce the role of both buff spells and magic items, since their benefits would strongly overlap.