Bill,
The newer bootloaders that are built atop the SDK follow the device firwmare update (DFU) specification provided by the USB-IF (official spec - http://www.usb.org/developers/docs/devclass_docs/DFU_1.1.pdf). Following the standard allows us to offer developers a clear interface to the bootloader with other operating systems besides Windows, such as Linux and OSX.
The original HID bootloader (from 2014) is a homemade protocol over HID. The original C# library for this is not compatible with any of the newer USB communications within the SDK. There aren't any missing features per se, but the HID link is quite slow compared to the newer implementation.
Mostly, the latest USB device stack also allows us to expand beyond just a generic connection. The new architecture allows for implementing any type of interface (e.g. mass storage, composite etc).
Let me know if you have any further questions.
-Tyler