For the elemental attunements, perhaps that it can't have any materia of an element that the crystal's element is either strong or weak against? Using the Earth crystal example again, that means that they wouldn't be able to have either Lightning- or Wind-elemental materia in their gear? Divine crystal wouldn't be able to hold materia of either the Holy or Shadow element, depending upon what element the crystal is (or, to be safe, it can't hold either Holy or Shadow, regardless of what type of Divine crystal it is). Cosmic not being able to hold any materia that confers an elemental bonus sounds reasonable (so that you still can hold something in it, even if your choices are cut down to utility materia) as well, possibly. Any of the boni from the crystal do not stack with boni from any enchantments or materia in them or any other boni innate to the character either (so you can't have a level 3 Fire materia in a Fire crystal weapon and get +3d6 fire damage for spending 1 MP, or your Ice crystal armor doesn't stack with your natural Ice elemental resistance of 5, so you're still going to have to spend 3 MP to get Ice resistance 6 against the one damage roll).
The non-elemental armor I've already specified that it works as normal against all elements, you just have to pay two MP for 1 point of Non-Elemental resistance, since for all intents and purposes, non-elemental damage is akin to Force damage in Pathfinder (which is a rather powerful energy type), or so I thought? It's in the last line about how crystal armor works. A level 20 character could spend 10 MP and get resistance 20 to all elements and Non-Elemental resistance 5, for example.
The main reason why this special material comes across as relatively balanced to me is because you're spending a limited resource for a few extra dice of damage that is already limited by your level (you're only spending five points at most when you're at 10th), on top of the monetary costs that come with it, which can amount to a small fortune at the earliest times you can afford the stuff. For the classes who are made to be out there and trading blows (Holy and Dark Knights, Red Mages, etcetera), their MP is an even more limited resource, and either they're going to be blowing it all on whacking a bad guy really hard, barely managing to survive the Firaga they just got nailed with, and having nothing to cast spells with the rest of the day, or they're going to be sucking down Ethers like they're going out of style, which is a pretty big hindrance to the other classes in your party that rely more on their magic. It's a very consumables-intensive source of damage or protection, especially if you wanna get into higher grades of stuff.
EDIT: Oh! Also, your mention of the deep crystal's extra damage? I was saying that the damage done with that was multiplied, not the dice, since the 2d6 was increased weapon damage, but after having a look, I'm pretty sure I was wrong there anyway.
The non-elemental armor I've already specified that it works as normal against all elements, you just have to pay two MP for 1 point of Non-Elemental resistance, since for all intents and purposes, non-elemental damage is akin to Force damage in Pathfinder (which is a rather powerful energy type), or so I thought? It's in the last line about how crystal armor works. A level 20 character could spend 10 MP and get resistance 20 to all elements and Non-Elemental resistance 5, for example.
The main reason why this special material comes across as relatively balanced to me is because you're spending a limited resource for a few extra dice of damage that is already limited by your level (you're only spending five points at most when you're at 10th), on top of the monetary costs that come with it, which can amount to a small fortune at the earliest times you can afford the stuff. For the classes who are made to be out there and trading blows (Holy and Dark Knights, Red Mages, etcetera), their MP is an even more limited resource, and either they're going to be blowing it all on whacking a bad guy really hard, barely managing to survive the Firaga they just got nailed with, and having nothing to cast spells with the rest of the day, or they're going to be sucking down Ethers like they're going out of style, which is a pretty big hindrance to the other classes in your party that rely more on their magic. It's a very consumables-intensive source of damage or protection, especially if you wanna get into higher grades of stuff.
EDIT: Oh! Also, your mention of the deep crystal's extra damage? I was saying that the damage done with that was multiplied, not the dice, since the 2d6 was increased weapon damage, but after having a look, I'm pretty sure I was wrong there anyway.