Probably not being able to re-sell a game disc if you want to sell it.
In a perfect world this issue should theoretically be moot as buying a game digitally *should* allow access to future versions of the game. Granted, it doesn't happen all the time, but the technology is already here to do that. For example, I bought Journey digitally on PS3 and it unlocked the digital PS4 version for free (about a year or so later). This also happened to the games Flow and Flower. Sony are pretty good with this sort of thing via their Cross-buy and Cross-save features. Whether companies will do these sort of consumer-friendly things going forward, well, that's the problem. Fair dos to Microsoft, though. They're doing some great things with BC on their consoles.