The USB Blaster uses a FT245 USB to parallel FIFO interface. The translation between the FT245 8-Bit parallel intreface and JTAG involves a combination of bit-banging commands, that can set each JTAG and additional AS interface line to arbitrary states and fast SERDES operation, that streams multiple bytes in and out without issuing a new command.
The MPSSE (multi protocol synchronous serial engine) of the newer FT2232 chip offers basically a similar mode of operation. It has been an obvious idea to utilize the FT2232 for an Altera JTAG programmer as well, and Sasco has done it in the BeMicro. (This wasn't possible without Altera support for programming the device driver on top of Altera JTAG Server of course).
As discussed in a previous thread, using this driver (and a respective configuration EEPROM), an FT2232 can be used as an Altera programming interface.
http://www.alteraforum.com/forum/showthread.php?t=20490 With the current driver, the BeMicro solution is about 50% of USB Blaster speed in AS programming, but considerably slower in Signal Tap II operation. I think it's rather a driver issue than caused by a more effective USB Blaster protocol, because the raw USB traffic is almost equal with both solutions, but I didn't yet check in detail.