Is my PCB layout ok? (ATMEGA32U4, WizNet W5500, Ethernet)
Generally crystal load caps are double the xtal specified load minus input capacitance. So a 12pF xtal might require 20pF or so, depending on the chip and layout.

Your LEDs are shown backwards. 

C2 has no polarity marking so I am assuming it's ceramic- you may need to add a small resistor in series to keep the 1117 stable under all conditions. It's a very old chip and datasheets don't necessarily warn about having ESR too low. The LM1117 (the original chip) datasheet (later revisions) contain this warning: 



I didn't check your numerous other points.