That is a bit problematic: the Xilinx PCB design guide calls for 0402 imperial size caps. Does anyone have a good feel what happens if that size is changed? If the caps should stay 0402, then my second question is: does it make sense to keep the 0402 caps for the FPGAs but make all other 0402 size devices larger (for the MCU for example) or is there no extra difficulty on using more 0402 packages than absolutely necessary?
In general, a smaller capacitor will be able to get closer to the pin and therefore do a better job decoupling. I think it would make sense to just use as few 0402s as possible: the probability of making a mistake soldering is just going to be increased for each additional capacitor. I don't think we have to think about it like reducing trace width or such (therefore raising the cost of the whole board). When these boards are eventually loaded by a professional shop, they won't even blink when we ask them to load 0402s.
Anyway, we need li_gangyi's input on this, because he's the one who'll be doing the actual soldering on this prototype.