100% agree with OP and many other posters, particularly:

1.) Unique materia akin to FFVII that adds new abilities, spells, etc.
2.) HQ synths that would add an extra slot or so to the gear
3.) Elemental resist materia that's actually worth a damn and would make a difference when fighting in a certain area, vs. a certain nm, etc.
4.) Being able to add/remove materia freely, which would remove the senseless RNG system from melding that's currently in place - but perhaps make it so you still need a crafter at a certain level to add/remove materia from the item
5.) Perhaps allow crafted gear to only max out at 3 materia slots, while dropped/raid gear will have 4-5 slots