Well, how about a weapon having a maximum of one stone, and stones can be combined to make more powerful stones.

For example:
3 fires make a "fire 2"
3 "fire 2"s (9 fires) make a "fire 3"
3 "fire 3"s (27 fires) and 3 "water 3"s (27 waters) make a flare
3 "earth 3"s (27 earths) and 3 "lightning 3"s (27 ligntnings) make a meteo
3 meteos (81 earths and 81 lightnings) and 3 flares (81 waters and 81 fires) make an Ultima.

Thus, you would have 15 different stone types, but only 15 variations of each weapon because you only get one stone per weapon. Also, it wouldn't be easy to make all your weapons Ultimas simply because of the sheer amount of time it would take. You could make the items drop rarely, but higher level creatures and bosses drop the higher level ones.

What is it they say about silence being golden?