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Are materia levels up-gradable at some point in the game either through a vendor, crafting class? For example can I take x3 or x5 level 1 materia and upgrade it to level 2 materia? I have a lot of materia built up and I'm just curious to know if its worth keeping the lower level materia.
Not really, no. There's a goblin you can trade 5 materia to, and he'll give you a random materia in return. Normally, you get materia of the same grade, but there's a small (~5% chance) that you'll wind up with the next tier up (for example, trading him 5 tier-3 materia will usually result in a random tier-3 materia, but with a small chance at a random tier-4 materia). It's not reliable enough to bother with in bulk. Your tier 1~4 DoW/M materia will always be nearly worthless.
Thank you for clearing that up for me. It's kinda of disappointing, but at least I can now free up a good amount of space on a retainer.
If you have any intention of completing the level 50 relic weapon quest line, you may want to hold onto at least the types of materia you would intend to put on the weapon. I ran into that small problem after I had cleared out below tier 4, had to spend a small pile of gil to get back what I needed.
Hasrat is definitely correct. There are a handful of fringe cases where "trash" materia is useful, so you may want to check the markets before you just sell them to an NPC vendor (though the last time I checked, almost all of them were pretty worthless). I suppose it's also worth mentioning a few other niche uses of "trash" materia...
• Spiritbonding: Gear will spiritbond faster if there's materia melded into it. The spiritbond increase is the same regardless of type or tier of materia. For example, some people will socket trash materia onto their DoH gear while crafting stuff in bulk in order to turn it into materia faster. Side note: If you are doing this, don't forget to try to unsocket your materia before you convert the gear into materia! There's no reason to waste perfectly good trash materia.
• Desynthesis: Desynthesizing gear with materia socked gives you a small boost in your desynthesis success rate. I think it's a 5% boost per materia (regardless of materia type or tier).
It's also worth noting that there are caps of how much of each particular stat each piece of gear can have. As such, there are situations where a piece of gear will not benefit from the full bonus of a higher grade of materia. In these situations, you would derive the same benefit from a lower grade, effectively meaning that using the higher grade would be a waste.