Minimizing Agricola setup/clean up time
How about a foamcore insert?  I just finished my Agricola foamcore yesterday. I haven't benchmarked the setup and breakdown times (yet). There are no zip top bags to open, it should only take a minute.  

I have friends who get a little tacklebox organizer for each game.  This takes more effort than that, but it's much more customizable.

For a crash course on how to make something like this, check out this video series: Using Foamcore by The Esoteric Order of Gamers.

Updated with a new version:
v1 v2