28/10/2020 -> rev 0.3

Schematics:

run ERC!
add ESD protection diode on USB data/power lines (https://fr.farnell.com/nexperia/prtr5v0u2x-215/diode-double-tvssot-143b/dp/1524157?st=PRTR5V0U2X) or similar
add small debouncing caps (100pF-100nF) on the switches (parallel to the PBs)
MIC5129 is a linear regulator, so it will dissipate a lot of power. Consider using a proper PMIC (power management IC) with built-in buck/SEPIC converter (high efficiency) and battery charger.
if the Atmega is powered from 3.3V from an external regulator, you should use a different connection of VBus/UVCC/VCC pins (see datasheet Figure 21-6.)
D1 has too much dropout (I assume it's silicon diode - 0.6 to 0.7V) for the regulator to provide +3.3V from battery power (+3.7V typical for li-ion cells). Choose a schottky diode or a FET-based reverse polarity protection circuit (google: 'mosfet reverse polarity protection', just make sure the diode has low enough dropout and the transistor - low emough VGS(on) to work from 5V).
SHLD pads in typical USB connectors should be connected to the GND.
Schematic is not consistent with the PCB. Where are the switches?