I can see a bug around your reset pin. The connection to Vcc from the switch that runs above the Atmega needs to be removed otherwise your reset switch wont work, and you will have direct short when you press the button.
The whole aim of the "pull up resistor" is to make sure that when you ground the pin there isn't a short and when the pin is floating its pulled up high, because no current will be flowing through the resistor and the voltage across the resistor will be 0V so Vcc will be at the reset pin when its floating.
You should also put some decoupling capacitors in across Vcc and Ground. I would put at least one 100nf across Vcc and GND and also another 100nf across AGND and AVcc. You could even put two in parallel. Keep them as close as possible to the IC.
These decoupling caps are important and I won't go into the technical details of why, but since you are using an RFID reader you should use them.
I see you are using PD0 or the serial receive pin for RFID_enable and the INTO pin for RFID_SOUT. I am assuming that it takes a serial stream of data (hence _SOUT) have made sure that you can produce that serial stream in software, because if it uses a standard SPI or even serial interface you can perhaps make use of the serial port on the ATmega.
Everything else looks good, it depends on what you are hooking this up to as well.
Are you desiging a PCB, if so keep the tracks as short as possible and try not to put the crystal and its caps close to any other switching signals.