First, how did the EF-S story beginn?
An APS-C sensor needs other lenses at the wide angle side. You can build them smaller, lighter an cheaper. So every maker of lenses (Canon, Nikon, Zeiss (Sony), Sigma, Tamron, Tokina) started to make those lenses. All of them stuck to the same dimensions at the back of the lens, as they had on a FF body, except Canon.
I think the most logic reason about why they did that was, that it gave them more flexibility in the lens design. A few milimeters more are welcome there. And why not do this? Which pro with a FF-Camera would ever mount those cheap APS-C lenses on their bodies?
Times are changing; some APS-C lenses cost over 1000$ and offer very good quality, while FF-Bodies are below 2000$ now. So many people are moving up from APS-C to FF. This causes the APS-C-Lens on a FF body (only for EF-S-lenses). But how big of a problem is this?
Sure, there are some photographers, who need to sell their expensive EF-S 17-55 f2.8 and EF-S 10-22mm (mine will be up for sale soon), in order to go to FF, and buy new wide angles and standard zooms. But be honest, when you move up to FF, you don't like to use your 17-55 f2.8 anymore. The APS-C lenses would only be there as long as you need to buy an all FF set. Then why would you buy a FF body, if you only use the APS-C area?