The crafting system is like the battle system: it's been repaired too many times with too many different end goals and needs an overhaul prior to ps3 launch in combination with materials production overhaul.

Many of the features in crafting were based on the very old system where the higher the quality, the harder the synth. Essentially the old system made level exponentially more influential on hq ability. When they nerfed that, they nerfed a lot of the rates to compensate. It's three systems layered on top of each other like a makeshift ancient city, not so much a cohesive, unified idea.