I wouldn't mind the Auto-Level craft system, not because I want to be handed things, but because spamming "Enter" does take away from the Classyness of a FF title. Actually making a craft is pretty good imo. The mini-game isn't too bad for making hard to make synths and HQ items (randomness aside). So there are some things that would make Auto-Craft less of an Easy Mode.

-DoL Items should be DoL specific (no ore dropping from Mobs, Branches, Grass, fish)
-Drop rate of alot of items will need to be adjusted
- Crystals and Shards should only come from Harvesting or Levequest Mobs and synthing fish (not random mobs)
- Amount of shards made from Synthesizing should be adjusted so Alchemy isn't the only Craft being played

I know it's not perfect but my line of thought is that
-(Buy Gil's) grind low level mobs for shards and crystals to sell
-Shards/Crystals are the biggest (Buy Gil) market
-(Buy Gil's) Grind Alchemy to make Shards
- Botters Farm Mobs for ore, coral, branches etc
-Havesting Bots are way more obvious than crafting bots

Summary - Harder to find mats and shards paired with Auto-Craft will even out Crafting. People that don't really want to craft, wont take the time to Harvest/ Find a Harvester that can supply them with mats. Harvesting bots are easy to spot and exile. (Buy Gil's) will have a harder time making gil to sell for real money

Besides, can't have auto-attack without auto-craft