Can't bootload ATMEGA328P-PU

Assuming you removed the connection from AREF there is just one obvious wiring deficiency. You really should have two 0.1 µF capacitors connected from VCC to GND as close as possible to the target. I've programmed targets without bypass capacitors so that is probably not the problem.

Given what you've posted there are just three possibilities left...

  1. Broken or loose wire.
  2. Clocking problem.
  3. Programmer's bitrate.

Only you can do anything about #1.

#2 seems unlikely. The capacitors are in range (12 to 22 picofarads). Everything appears to be connect correctly. There are two clocking options in boards.txt (internal oscillator and external crystal / resonator) so it is unlikely the fuses have been set to something "odd".

Which leaves #3. Your programmer has to be configured for a bitrate of 125K or slower. The avrdude command-line you posted does not include the option to set the bitrate which means it could be anything. I assume your AVRISP MKII has a way to set the default bitrate. I suggest ensuring it is set to a reasonable value.