I don't know if an updated console (ie redesigned) console is much better than an emulator from the perspective of accuracy. Also, the newer systems are much more complex and I see this as unlikely. However, it would be cool if companies would 'open-source' their older hardware and charge royalties on people selling updated units. Sega has already done this in a few markets (sort of). Also, I think your idea of adding a USB interface for controllers would drive up the price too much -- better to just keep the original ports.
Unfortunately, for most older systems, the sought after games tend to be much more expensive, and it's those that people want, not updated hardware. You could include some games in the system itself (in the case of the cart systems), but then it wouldn't be much different from the DTV devices that are so common these days.