Thanks for your quick and helpful comments Crossroads
I don't see any decoupling caps(100nF) on the power pins for the various devices.
I didn't know about this practice, could you please tell me more about it? or suggest reading? and I just put it on the Vin pin of a device? or between VCC and GND?
I see a diode on the FTDI power interface - if someone plugs in a 5V USB/Serial adapter, that will put 4.3V on the VCC line, could be a problem with the rest of the board appearing to run at 3.3v based on the power header. Most 3.3V devices only want 3.6 to 3.8V Absolute max.
You are right, those 4.3V go to the Regulator Vin. Was that wrong?
Standard anymore is a diode across the reset pullup resistor to dissipate any spikes to the Vcc pin and not put the uC into high voltage reset state.
I've posted the Atmel Application Note on that a few times.
I'll do that.
Your ICSP header is in a non-standard location. Could be a problem for some shields.
You're right, but I'm afraid I can't put it where it should, at least in this design.
Rx & Tx need to be swapped on the FTDI header.
I'm a little confused here: I thought the FTDI's RX goes to arduino TX and vice versa. Is it wrong?
What is the Aref solder jumper for?
I was not sure if I must set my AnalogReference to external and connect it to VCC so I offered myself that possibility later.
Are there top & bottom layer ground planes? Hard to tell from the drawing.
Bottom plane is, but not the top. Do you advise to create a GND polygon on the top too?
Move the signal names away from IC3, can't read what they are.
Will do, sorry
Overall, I'd say Good start.
Thank you sir