Set bonuses would be nice but they don't really solve any of the problems with the materia system, such as:
-Powerful materia and multi-melds making dropped/quested gear from real content unappealing
-Unmeldable gear that is strong enough to stand on its own making materia eventually fall out of use
-Powerful gear being obtained through luck and gil alone, with no need for the player to ever step outside of the city
For the materia system to really work ALL GEAR needs at least 1 meld enabled - no matter what color its name happens to be. This creates a standard set of stats (for example, Paladins will always have access to enmity on their belt and weapon regardless of what the actual stats on their equipment are) and allows for real customization options (in the case of a Warrior picking between enmity, parry, strength, etc. for their weapon).
Having U/U items act only as filler gear until you can manage to multi-meld a generic crafted piece is 100% backwards and completely ridiculous. At the same time, having the entire materia system act only as filler until you can get a good U/U item is a waste of a system and developer effort. What we have now is a system with good intentions (give max level players a reason to go grind via spiritbond and keep crafting somewhat useful by churning out generic gear) but really poor execution (Multi-melds producing insane gear via lottery, Gla/Con/Thm dropped weapons being useless in their main roles, unmeldable gear outside of a select few pieces being garbage, doesn't actually remove any gil from the system)
The other problems with the materia system like the overabundance of Mind III and Manathirst floating around can be dealt with in a number of ways. One idea I've seen tossed around is combining two of the same tier of materia to create one random higher tier materia. For example, you put a Mind III, a Parry III, and 500 gil into a goblin's machine and get a Dexterity IV. For two IVs you could just produce another IV, or maybe have them grind up into a crafting reagent or melding catalyst. Just whatever to get them filtering out of the game.