This is how ready Xplained Yourself rev. 1.1.1b looks like:
It works great. I tested it with ATmega328P and ATtiny1616 as far. It can program and debug, no surprise here :)
I didn't have ferrite bead so I replaced it with piece of wire, also I didn;t have one 47u capacitor, so I replaced 1117's output cap with 1u ceramic one. I'll order them when I'll have more parts to buy.

I made few minor mistakes:

• LED name - is programming indicator not power. (I added power LED with it's resistor across C4)
• Few ground vias are not connected.
• No via is tinted.
• Few names are hidden beneath footprints.

I changed that in 1.1.1c. I also added some improvements:

• More ground fields for better screening signals.
• Power LED.
• Target voltage sensing LED.
• Test point for ATmega's reset (external programmer is needed to set clock out fuse, which is necessary for routing clock signal to CLKO pin).
• 5V protection Schottky diode. Schottky diodes have low drop - 0.3V. That means, output voltage is 4.7V, which is safe for 16MHZ and 20MHz AVRs, and should be enough. 
• Signal names on silkscreen.
• I moved few traces I was afraid could touch others.

Here are pictures of new board: