Love the AT90USB1286, was my first microcontroller (Teensy++2.0). Still use a Teensy++2.0 for occasional tests, so if there is some behaviour you want someone else to test on a different AT90USB1286 board, do feel free to PM or email me.
The
datasheet says USB D- (2.2.10) and D+ (2.2.11) need 22 Ohm resistors (in series, between the USB connector and the pin), and UCAP (2.2.14) needs a 1µF bypass capacitor to ground.
The older Atmel version datasheet (which you can find at
PJRC) has additional information, so if you reuse older chips, there might be slight differences. For example, the older datasheet highly recommends 10µF from VBUS to ground at the chip, but the newer does not. I'm hoping the later device iterations got a better internal voltage regulator or something that made that recommendation obsolete, but personally, I would reserve a 0805-sized pad next to the chip for that since you seem to have the room, just in case.
Me like the per-button diodes

but would also prefer thicker traces everywhere for purely mechanical reasons. Soda spills and such, you see.
I would also consider a 1µF from Vcc to ground, and maybe even a ferrite in the +5V supply line northeast of C6 (with a thicker power trace!). Are they
required? No!
But, it seems that development boards that do have them,
feel stabler in my uses. Perhaps I'm imagining things, or perhaps my cheap USB leads are antennas in disguise, or it is due to something completely different and not just high-frequency noise in my +5V USB lines like I suspect it might be; me being just a software-oriented hobbyist and not an EE at all. I do regularly use cheapie eBay <$10 USB isolators based on ADuM3160 and cheap isolated DC-DC converters, so perhaps that is core reason in my case; they do have high-frequency switchers and not many components for filtering. But, since a ferrite bead with less than 50mOhm DC resistance, maximum DC current well over an ampere, and an impedance over 120 Ohms at 100 MHz costs less than ten cents in singles, (and in the same vein, since you already use an 1µF cap for the UCAP pin, adding another for VCC) seems obvious belt-and-suspenders to me: not necessary, but might make the difference between the keyboard being rock solid and sometimes cranky due to noise on the USB 5V line. You can always omit them at board build time to reduce the cost (although the ferrite bead would need to be replaced with a short).
Edited; forgot to mention: Microchip appnote
AN_7602, also known as AVR271: USB Keyboard Demostration, uses the STK525 starter kit to implement an USB keyboard. The STK525 series 6 uses ATmega1286, so the USBKEY_STK525-series6-hidkbd-2_0_3-doc.zip in the AVR271_USB_Keyboard.zip that you can download off that link, is more or less directly applicable to your project here. Even if only as a reference into how Atmel/Microchip envisions the MCU to be used for this, it is certainly informative.