Lumber (and lots of miscellaneous stuff) storage and crowded by tools & work benches are my main issues, too. Additionally, with my shop still in the remodeling stage, all the dust collection is not yet in place, so cleaning up, in most areas, is an unpleasant additional job/inconvenience, in itself. This scenario is compounded when I have more than one project going at a time, i.e., another item to work around/avoid, which seems to continuously be the case.
As for as the rustic look of the shop decor, I've had the same sense for a long time. I have a start on that, though, with log posts as beam supports down the middle of the shop. I don't have too much concern with heating, so a pot belly stove is not on my wish list. I have thoughts of a porch swing under the backside overhang area, once all the lumber cache (mostly framing lumber & ply products, now) is either moved to the inside storage areas or used in the remodeling. I suppose, by the time I get the swing installed, I'll be too old and lazy, so it'll be time for me to just go sit and do nothing, anymore.