Placement of the crystal
I recommend that you try to get the crystal closer to the pins on the MCU, as the inherit capacitance in the wires can generate a bit of a problem. I would rotate the MCU, and place everything so that the crystal is as close as possible. In this case, this is more important than having the decoupling capacitors for the vdd on the mcu close to their pads, as these capacitors are much bigger, and the inherit capacitance in these lines wont affect quite as much.
When you do the final version of the PCB you should follow rule of thumb order to make everything easier. Begin with placing the MCU and the crystal, and wire these up. Then place everything else, and try to get the decoupling resistors as close to the MCU as possible. After that you wire all the critical data lines (USB, SPI) and try to draw these so that the corresponding data lines (MISO, MOSI, SPI, D+, D-) goes along side each other to make sure they are approximately the same length. After that you wire all the other data lines (interrupts, chip select and stuff like that). Then you draw the power wires and finally the ground wires. That should make everything quite neat.
Alternately, you can measure the capacitance in the wires by calculating the width and length of these (kicad comes with a pcb calculator you can use), and change the crystals corresponding capacitors values with the formula C = 2*(Cload - Cstray)
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