For the caps in the FPGA section, these are based on the recommendations in the XIlinx PCB design guide. I would opt not to change those. The resistors in the FPGA section were chosen by me: no particular reason for this size, I just wanted something small that should still be able to stand the dissipated power. For the PSU section, li_gangyi chose the component sizes. I replaced all packages with something found in the rcl library (I prefer to have a common look of the symbols and I try not to have several non-standard libraries in the project). If any of the parts there strike you as odd, I either made a mistake when doing the conversion or you should get li_gangyi's input as to his package choices (I am really bad at analogue stuff, so I wouldn't want to comment). As for the MCU section: I replaced most of the choices in O_Shovah's original design with something else. The idea was to minimise the number of different components: for example in several places where 100nF would have been sufficient I wrote 470nF instead so as to use the same parts as for the FPGA.
You've done a great job keeping these various schematics clean and uniform, and reducing the number of different components. The only strange ones to me are the PSU ones, so we need li_gangyi to answer about these.
I added most parts from the FPGA, PSU, and MCU schematics to the BOM database. I also created BOMs for each. A few questions that came up while doing this:
1) Surface mount power connectors? These would really be much better as through-hole, for strength.
2) I think I remember li_gangyi asking us to keep components above 0402 (1005 metric). Can these little guys be switched to 0603 or larger? For prototyping and debugging, it's also better to keep things larger (easier to probe and rework if needed).
3) Are we using the LMZ22010 or the LMZ12010? I'm seeing some confusion in the various schematics here. The difference between the two seems to be the SYNC pin, which we aren't using, so I don't see why we shouldn't use the cheaper one.
4) Speaking of the LMZx2010, the datasheet is calling for slightly different resistor values on R_FBT and _FBB. Am I just reading this wrong or was this a mistake?