Will you have a feed or tack room?
I think, if it were my property i would run a sacrifice paddock completely around the back and sides of the barn. Make it big enough that a tractor will fit through the gate should you need to add dirt or remove manure. This would be one large paddock, if you need to cross fence it i would use electric fencing so it is portable. That way you can decide if you eventually want a more permanent fence or not.
The front of the barn would be where cross ties are for grooming and saddling. You might want a 6-12 ft overhang for that. Perhaps a wash rack area in front as well. This gives you storage in front of the barn as well, or an extra area if you eventually get another horse.
As for storage for wheel barrows, you certainly could add a space between the stalls. It definitely would reduce stall arguments.
If you really want ventilation, i would not build solid walls. You could run 2 or 3 boards at chest height, but leave an opening from the boards down. This way a shop fan set up at one end can blow through the entire barn at once. No solid stall doors- use those small metal gates. You can also use 2 sliding boards with a pin lock instead of stall doors. I like stalls that open on both ends, but i can live without that feature.
If it were me, the grumpy horse would get her own stall on the end with a solid wall and an individual fan. In the storage space next to her i would put a drum fan. The rest of the barn would be open like described for the best possible ventilation.
i don’t see a benefit in adding small runs. To me, that is going to create an area where manure will accumulate and possibly mud. If you need to keep everyone separated, that would be time for portable electric fencing. As for the sacrifice area, i would make it a long rectangular area with the stalls on the narrow end of the rectangle.
My horses are very cleanly in their sacrifice area. All manure is deposited in the far back of the paddocks, while food and water is up front. Making your sacrifice area a long retangle, will help keep the manure farther away from the barn. Even my pony (who was a piggy) has somehow gotten with the program and now deposits his messes in the back.
By biggest mistake was making the sacrifice areas too small. You really want it big enough to keep the horses farther from the manure, and you also want that manure spot to be somewhere sunny.
My horses all have individual sacrifice areas just because between the hard and easy keepers, and the bully, it was difficult to keep everyone together. Shade is another issue. One paddock has nice shade in the morning but is sweltering in the afternoon, and the other paddock is the opposite.
If you want or need shade, plant something now.
Consider drainage. I would add fill before having the barn installed. Get someone with a tractor to spread the fill over your sacrifice area at a slight slope. You want everything to drain away from the barn. If you do this correctly the manure (and excessive rain) will wash downhill and away from the barn. Obviously this isn’t always in the budget, but if you can afford to do it, do it.