The most glaring not connecting up the built in Ethernet and wiring multiple pins together effectively limiting external ram use come to mind. I have not yet received the one I ordered but made some in the shop, I think you really limited yourself in trying to keep the the mega form factor which in itself was trying to keep comparability with the previous generations. I'm already thinking of a lot of kit that does not have the correct values for current limiting resisters where a 3ma is not going to be enough. Now granted I think the breadboard compatible form factors make more sense for a hobby/learning device. I love the ecosystem you guys have created but I've never been thrilled by the hardware. That is the strength of open source hardware I can just pop up eagle make what I want by building on the great works you guys have already done.