[...][...]
My understanding was that it is possible to brick the Atmels. Can you confirm (or better: rebut) this?
What exactly would you define as bricked? If you had a USB bootloader and accidentally overwrote the firmware, you would need to reload the bootloader with a programmer (or have the motherboard do this). The only "bricking" I can think of with the AVRs is if you accidentally lock the flash memory or disable the RESET pin (needed to load new firmware). These can still be recovered from by using a special programmer.
Bricked would mean either completely unrecoverable or not recoverable without desoldering from the PCB. My understanding was that, like you said, the fuses can accidentally be set to lock out the RESET pin. But I thought this is completely unrecoverable, even by a high-voltage programmer. Or isn't it? The curious thing is that the different Atmel chips have different programming strategies, and I only read about the one for the ATtiny. For a USB capable MCU: no clue.
The only real problem I can see with the AT90USB82 is that it doesn't support 2.5V operation.
Is 2.5V operation a requirement? Can USB run at 2.5V? I don't think so.
Important are the IOs that go to the FPGA. While the Spartan 6 can be operated at VCCO = 3.3V, this may not be the preferred voltage. And other FPGAs for a second generation of DIMMs may not support 3.3V at all. Basically, it's not a show stopper, not even a very huge demerit at the moment, but it is something to keep in mind when comparing otherwise nearly identical MCUs.