My opinion is that we need lots of shallow drawers and flat surfaces.
Shallow drawers make it easier to find stuff than large cabinets or shelves (where things get stacked, put behind one another, etc). Also means that tools can be spread out so they’re closer to the relevant machines.
Flat surfaces near machines just give a place to put stuff while you’re working on it, rather than getting out a bunch wrenches to set up your fixtures on the bridgeport and leaving on the mill table (or running back and forth to the toolbox each time you need to adjust it).
We used this behind (i.e. your back is to it while running the mill) the mill area of my college shop and it worked very well for us.
Additionally, it’d be nice to spread out the measurement tools, keep a set of cheap calipers and a few small mics at each mill/lathe (since you pretty much always are going to need them). We could have a drill index at each machine as well (not a huge fan of the small cabinets where drills are easily put back in the wrong spot).