The MSEL pins are powered by VCCINT

I think, in most practical cases, the difference between using VCCA (as suggested by Altera for Cyclone III) and VCCIO (as it has been ususal with previous FPGA families) won't matter much. A problem arises, if the supply nodes power up at different times, and particularly VCCIO after VCCA. In this case, MSEL, that is evaluated first when the VCCA and VCCINT supervision circuit releases the internal reset, may be read in wrong. In a design, where VCCA is generated by a LDO from the 3.3V supply node, this e.g. can't ever happen.