Ore System - World Generation

[Methes]

Larger Veins and higher Quality veins should generate deeper underground, while small and poor ones on the surface.
Size and Quality chance increases with terrain altitude - mountains have higher chance, oceans have less chance - this prevents people from cruising oceans to find large and rich veins. Also makes mountains more appealing to dwarfs.
MC world generation offers very little Y altitude to effectively generate rare materials deeper. Defining Y range for different materials and altering the height accordingly to Quality and Size is probably desirable though.
PFAA ore system is based on Geology and rock types and layers, right? I'm not entirely sure how to put that together with altering heights and mixed ore veins.
Larger veins could have small ore rocks on the surface hinting present Vein deep underground. Like in TerrafirmaCraft.

[Kaethen]

On the problem of the Y axis: Why not just raise the ground level in general from 64 to 96 for example? After all, Y goes up to 256 and most of that space remains unused, so raising the ground by 32 blocks will give you much more space to do exciting stuff underground witht he terrain generation while leaving more than enough space above for large buildings.

[lawremi]

The goal of PFAA is to generate rocks, ores and minerals in realistic patterns. That said, there's some leeway. For example, PFAA already generates small "hint veins" around some of the more important ores. These hint veins could be made to contain lower density ores. Not sure I want to make everything valuable deep though. Seems too simple.

Raising the ground height is outside the scope of PFAA. That's something left to the biome mod.