You assume everyone wants to make everything. Plenty of players fill a niche and sell piles of their product to afford all the other ones they need- a functioning economy. Even if I push all my crafts to 50 and can make everything, I'll still be more likely to do the above rather than run to Northern Than to grab some ore, then to Southern Grid to grab some logs before crafting my new sword.

Shards and their rarity are currently a problem. Those should not be the greatest limiting factor in crafting, it should be the materials themselves. Whether it be you yourself running outside to grind out shards for two hours or some guy you pay for his time. However, solving that problem is a huge undertaking and SE needs time to work on it. RMT's flooding the market certainly aren't all good, but they aren't devil-spawn either.

Also, you certainly can flip those shards. I for one would never buy a stack of 10K even at 10 gil per. Buy his stack and dole it out in 1K stacks for 15 gil.