One of the first microcontrollers I ever programmed was a
Teensy++ 2.0 with an Atmel AT90USB1286-MU. They are still manufactured by PJRC, and widely used. The HalfKay boot loader used in the Teensy++ 2.0 is proprietary (allows uploading a new firmware via a HID connection, thus needs no special drivers installed), and I don't think the gerbers are open either; but the
schematic is here.
I have not created my own AT90USB1286 board, nor programmed one, except as a Teensy++ 2.0 using the HalfKay boot loader. I basically programmed my Teensy++ 2.0 in Linux, using avr-gcc, avr-libc, and TeensyLoader (for uploading via HalfKay).
I do recommend using a Teensy++ 2.0 for prototyping, even if you end up doing your own board, due to the large amount of existing code and examples for your use case.