I suspect the "ledge" to which you refer happens because the foundation transitions to a framed exterior wall. I understand the logic of the designer and it will not cause loss of floor space to have a uniform wall.

Personally I wouldn't think the "deep" windows would look unattractive as comapred to a ledge. You could use the sills as display locations, to grow plants or some other purposeful application. It's how you want to use the space. One family I know has a very deep ledge which they use as their buffet table when entertaining in the basement.

Our basement is a standard one with limited windows. We have some conduits which caused me to set one wall about 3" out from the foundation because I just didn't like the thought of a soffit to hide them.

Your house and your choice but I would probably go with a standard looking wall. Good luck.