Based on your responses, I've attached some modifications, but I have some questions.
On the FTDI connector, your pin 1 should be connected to the ATMega328P RESET pin via a capacitor, not direct connected. The FTDI signal is DTR and will keep the Moteino in constant reset without the cap.
Duh! Bad miss on my part!
Not a problem, that's why you have multiple eyes looking at it...
The RFM69 footprint is actually bigger than the Eagle Model and you have the NC pin on the RFM69 overlapping the VBat+ via in the vicinity of U2. I'm not sure this will harm anything but it should be checked...
I nudged them down a bit. You're just concerned that the radio will be covering the via? I've only left those exposed as test points.
I am concerned that the radio pad could short out with the via. The RFM69 datasheet says it's an NC pin, but that it 'should be connected to ground'. Well, if it's truly NC, why would it need to be connected anywhere? Maybe it's a test circuit, maybe nothing, but it would be safer to avoid shorting to it, IMO.
Optional: A potentially useful thing is to monitor the charge pin on the MCP7383x device, but you can't do this with the MCP73831 since it's Charge pin is pushpull output. If you use the MCP73832, which has open drain output, and tie the LED/resistor to 3.3V instead of the 5V supply, you can monitor the signal with a spare input to the 328P.
I took a look at the data sheet, and frankly, I guess I don't understand "open drain" vs. "tri-state" and how I could actually implement that in a useful way.
An open drain pin can only pull current to ground, while a push-pull pin not only pulls current to ground, but supplies voltage to the pin. In this case, the MCP73831 supplies 5V to the Charge pin. Not a problem if you only have an LED load. However, if you want to monitor this signal at the ATMega328P, then you'll need to drop it to 3.3V max. The simplest way, then, is to use an open drain device with the LED pulling the signal up to 3.3V instead of 5V.
I've attached an example below. In this case, the 'BAT_CHARGE' signal is tied to pin 2 of the MCP73832 and to the D1 pin as an input to the processor.
Tom