And having to use level shifters is very annoying. I just looked, though: the MSP430F5528 (and comparable chips) has several banks of GPIOs, but there is only a single supply voltage for IOs. And if you use 2.5V for the FPGA connections, you cannot use 3.3V for the connections to the DIMM bus (except for the USB, of course).
I see now what you mean. The MSP430F5528 has built in level shifting for the USB lines, meaning the MCU will run at 2.5V, but shift the USB I/O up to 3.3V by means of a built in LDO on the USB input voltage. That seems like the ideal behavior for us. As long as someone else is willing to work on the firmware for this, I think it will be a good MCU for this design.