Your new layout is a no-brainer. If you want into the majority of bathrooms this is the layout, shower is always along the back-way. Having it up front by the pocket door just closes too much in.
Sky light is a bonus and an awesome feature in a bathroom, I would just spend the money and make sure its vinyl/aluminum/stainless everywhere or its going to be an issue in short time.
If your going to tile the floor, why not tile the shower and do a roll-in? I'm not seeing the benefits of a shower basin. I would go tile all the way through the place and right up to the ceiling around the shower.