Everything in the one place.
You say that your keggerator and other fridges are in the house. I'd make room for them in the brewery. Maybe the keggerator in the house, but everything else in the shed.
I have a small dedicated brewery, but dont have enough space in there for everything. The bane of my life is running up and down stairs and from one end of the house to the other to get the bits that aren't in there. If it was all in the one room... mmm I dream of that
Apart from that.
A big double sink - really big so you can fit your whole boiler in there, and one of those pull down commercial taps on a spring, like the dishwashers have in a pro kitchen.
Overhead power - the dedicated 20-40 amp circuit that people are talking about. But wired in so that it comes in high and things hang down. Then you dont have to worry about anything electrical being dripped on or lying in a pool of water
Floor drains - but not just floor drains. Build your shelving and anything else so that it has a 6 inch gap under it. Nothing should sit directly on the floor. That way you can simply hose under everything right up into the corners, and it all washes down the drain. You can also get in under everything with a scrubber/mop. Cleaning's the hardest bit of brewing, make that easy and life will be better
Good ventilation - so it doesn't get too hot to brew in summer. AC if you get excited.
Continuous hot water system - Instead of a HLT, one of the continuous gas hot water systems that has been tinkered with so you can dial it to give you mash temp water. Or at least so that you can flush/rinse/hose with hot water and you dont have to heat it all up with your kettle/HLT.
Thirsty