I like the idea of building around the run in shelter, but because of where it sits, that would be very difficult. Our land is slightly highly, so there is a very slight incline in front of the shelter- we already measure to try and build forward (so that it would be a little deeper, back when I had 3 horses) but that would require a lot of digging. We also have our paddock and pastures kind of surrounding the shelter.
And I really don't care about having to haul hay, grain, shavings, etc., out to the shelter in the winter- I do that anyway, everyday, even though they're not stalled. We have hay storage in our garage, and the paddock/shelter/fields aren't that far from the house at all.
Nickers2002- is that an aisle that I see in from of your stalls? Because if we were to make stalls, it would be literally dividing the shelter that we have in half- when we'd open the stall doors, they would step directly outside. Your shed looks really nice, by the way. :)