Without thinking about it too much, a pretty good thing that I thought of as soon as I saw that Andy Collins line was this:
Completely get rid of magical "ammunition". You need to buy a Magical launcher (bow, crossbow, sling). Everything "fired" from the launcher is a "magical" projectile.
There you go, problem solved. So now every arrow fired from a +2 Bow gets +2 to attack and +2 to dmg, and of course works against a creatures DR of "+2". *Same thing* as if it was a LongSword, just from range. Also, the player has to keep buying arrows. How many arrows can that player carry? Make them keep track. Sure they can use extra-dimentional holders, but that costs some money to do that, and melee's don't have to pay that.
This also gets rid of having a "+1 shocking, acidic, fire, sonic, xxx, yyy, zzz" bow, because it's only ever going to fire +1 arrows. Edit Greater Magic Weapon so that only the bigger bonus applies. You have a +1 bow and get a +4 GMW cast on it? It's a +4 bow. Also, you know how weapons can only have a total of +10 enhancements? Make GMW abide by that. If you have a +1 bow with 7 "abilities on it, that's a +8 weapon, so the most you can get out of a GMW would be an additional +2.
There you go, pretty quick and down and dirty rules that I think are pretty damn effective, and good. You no longer have an archer firing with a +10 from his GMW'd (+5) bow shooting GMW'd (+5) ammunition.
Anyway we can get the designers to look at this?
Afterthought- the only problem I see with this, is the new DR changes (which I won't get into in this thread). How are they expecting 3.5 archers to deal with this? Will there be "cold iron" arrows? Will there be "xxxx" and "yyyy" arrows? I sure hope they're thinking about that sort of stuff.