Layout wise, it's OK but it seems to me like you could have done quite a bit better.
For example on the 2Shapes board there's lot of space not used properly.
For example :
U1 could be moved up a bit and a bit to the right ... to have straight traces from the pins to the header. Lots of room unused to the right of that IC.
U3 could probably be rotated clockwise 90 degree so that the +12v trace doesn't go under the chip and then below the chip, breaking all that ground fill
IF you don't rotate the U3, those C12 , R11, R13, C3 could just as well be rotated 90 degrees and aligned for a prettier look
You could rotate that D9 180 degrees and have the ground side land above U1
Maybe bring C6 closest possible to U1 and have trace going to D11 and R17 go above D12 and have +5v go under those two.
Also D11 and D12 or D9 and D10 could potentially be replaced with a 2-diode package, for example
BAT54S but then your design would no longer be 100% through-hole... and i guess maybe your diodes need to do more than 200mA?
Also do you need capacitors for Y1 or that's something with those capacitors built in?
Feels like you had everything snap to 0.1" (2.54mm) but you could do better positioning by setting that to 0.05" (1.25mm)