I came across the Teensy microcontroller http://www.pjrc.com/teensy/
, which is like, but not quite compatible with, Arduino. There is a plug-in for the Arduino IDE to use it for development.
Rather then using a serial emulation for communication with the host (with several limitations), it uses native USB and can (theoretically) operate at full USB-2 speed.
The software library allows you to program the Teensy to act like one of many standard USB devices (keyboard, mouse, HID, midi, storage, ... ), thus using the default host driver.
A few weeks ago I bought one, but have not used it yet. All I can tell is that uploading the morse-blinking demo from it's tutorial was blazingly fast. Setting it up under openSuse 11.3 linux gave no problem at all (quite different from Arduino).
One type has 12 analog channels, the other 8, so you might end up using 2 controllers. You can connect these using I2C as it uses diffferent pins then the host USB connection.