Currently the system in place only limits the value of weapons and armor.
Sloting enhancements into prefix and suffix limits combonations that would be useful, and limits the damage a weapon can do. Perhaps this is intentional.
Bound named items do not have this limitation, example; Retribution. Lawful, pure good, Holy. A random item can never have holy and law/chaos, or any elemental effect etc. because they are all prefixes. Yet this rule is bent for named items.
Really, perhaps it is time to scrap the prefix/suffix limit and just make everything an adder. Vorpal is +10 levels, Flame is +2 levels, Holy is +4 levels etc. Same type enhancements would be excluded, so you could not have 2 elemental adders, or true law and chaos etc.
A level 12 weapon should do level 12 damage, currently that is almost never the case, and many useful possibilities are not possible simply because two things that could go together are both prefixes or suffixes.
Also a True Neutral weapon effect could be added. 1d6 damage to one step removed (Neutral good, Chaotic Neutral etc), and 2d6 to something two steps removed (Lawful good or chaotic evil).
One argument against this change would be that weapons would become 'too powerful'. one possibility might be to separate damage adders, from special effects. So maybe you cant have a true law, flaming, pure good, holy, giant bane sword....but a Transmuting flaming pure good weapon....
Maybe limit the total damage dice to 4d6, and any other adders have to come from special effects or materials like Everbright or Banishing or something like that.
It is already hard enough to find a decent weapon randomly, a change like this would at least increase the odds of liking something you find.