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.
So long as you stick to only reprogramming these USB AVRs via the factory-preprogrammed USB bootloader, I don't think you can brick them. Which is fortunate, because recovering from a disabled RESET pin is apparently a pain; it requires a high-voltage parallel programmer that has to connect to pretty much all the pins and apply 12V to the RESET pin, which makes doing it in-circuit just a tad tricky.
The shipped bootloader is a bit annoying in that you have to manually hold a particular pin low during reset to enter it, but that's no big deal unless remote firmware updates are a requirement.
Is 2.5V operation a requirement? Can USB run at 2.5V? I don't think so.
Yeah, it just makes doing I/O interfacing a tad more tricky. As Olaf said, most of the FPGAs we're likely to use can run at 3.3V for I/O anyway, and if necessary level shifters are an option. (Looking at the Kintex-7 data sheets those support 3.3V on a subset of the I/O pins too.)