I feel like the recombinance problem could be solved pretty easily in a new edition.
A lot of buffing effects are much more complicated than they need to be. As has been mentioned, barbarian rage is a good example of this. Rage primarily gives a bonus on attacks and damage, as well as hit points and Fortitude saves. However, it also give incidental bonuses to a large number of other things which are not particularly important in the context of a short-duration combat buff. Rage could be changed so that it gave a +2 bonus to attack and damage rolls and temporary hit points equal to twice your barbarian level. The primary effect of barbarian rage would remain, but the changes that need to be made to your character when you used it would be simpler.
Another factor making buffing effects more complicated is the bonus stacking rules. The game would be much simpler if there were stacking rules inside a class of effects, but different classes of effects always stacked. Here's what I mean. Lets say I have a normal array of defensive magical items, and I have
protection from evil cast on me. I need to check to see if I have any resistance bonuses to saves or deflection bonuses to AC from my items to see what effect (if any)
protection from evil has on those statistics.
I would make two major changes to this system. First, I would reduce the number of bonus types. Many bonus types are so uncommon (such as sacred or luck) that they essentially stack with everything. I would convert all bonuses of these types into unnamed bonuses. This would leave me with armor, shield, natural armor, dodge, resistance, deflection, and enhancement bonuses (there would be a design rule stating that no new bonus types are to be added in rules expansions as well). Second, I would change the rules so that stacking rules only apply within their own class of effects. For example, two magical items providing a deflection bonus to AC would not stack, as they are both magical items. However, a magical item and a spell providing a deflection bonus would stack, as they are different classes of effect (magical item and spell). This would mean that you would only need to check magic item stacking when you change your magic items, not every time a spell was cast upon you, and you would only need to check spell stacking when you had more than one spell effect in place.
The final problem is short-duration buffs require more bookkeeping than seems needed. I would change the duration of short-duration buffing effects (loosely defined as buffing effects with a duration of less than 10 minutes/level) into subjective durations, such as "1 encounter" or "1 combat". That way, the primary balancing factor of short-duration buffing spells (the actions lost in combat) would be maintained, but the need for tracking very short durations such as 3 or 5 rounds would no longer exist.
Another option would be to eliminate stacking rules, give linear costs for magic items bonuses (instead of exponential costs), and make sure all combat buffs only last for 1 combat.
Finally, there needs to be a
free, web-based utility for adding templates and HD to monsters.