Changes we made:
--We made the whole thing a little bigger -- we wanted to be able to house a few more hens.
--We made the whole thing a little taller. We are using deep litter in the run as well as the henhouse. We wanted to make sure that there was enough headroom when the litter built up.
--We used plexiglass, not glass for the windows and made them completely removable for maximum airflow/ventilation in the summer. We also made the windows bigger.
--We added the screened door between the henhouse and run. This adds a great deal more ventilation, and the door opens to allow us to pull bedding from the henhouse directly into the run when it gets too deep/soiled in the henhouse. We also throw our leaves, weeds, lawn clippings, coffee grounds, food scraps, etc into the run. (Everything that used to go into the compost bin.) The run does need to be wrapped in plastic or have winterizing panels like in the original plans to keep the wind from coming in that screen opening (where I live it can get very cold -- below zero. In a milder climate you could skip the winterizing)
--We added a second human sized door on the other side of the run. We may, in the future, fence off a "pasture" area where the chickens can be out but safe from the dogs that are numerous in the summer. (We do allow them to free range as well.)
--we used plywood for the henhouse floor. Whatever was used in the plans was just too $$$ for us to justify.
--We also used narrower trim boards, again to save $$.