Nothing leaps out at me as being wrong particularly. That said, I'm lazy and I would replace much of this with an Arduino nano board. Taking the parts cost of just the mega, ch340, fuse, ldo and the crystal and regulator I come up with $7 US for the parts without the time to assemble and program the bootloader. For about $2.75 US (from ebay I assume the same on other sites) I can buy an assembled and bootloader programmed arduino nano (5V 16 mhz though, there doesn't appear to be a 3.3V version, although there is a conversion tutorial to 3.3V on the net). For that you get the usb/micro combo with the bootloader programmed on a smallish board that you can replace much of your circuitry with. Much better chance that it will work first time than trying to build your own from scratch. If you can use 5V rather than 3.3 even easier.
Peter
