It depends on the power pin to which ur decap is connected to and your GND plane routing.
It would probably be one of the core power supply decoupling caps. The ground plane is uncut, except for the vias running through. Actually there is 2 ground planes. One on each side of the board, below the component planes.
What would be the preferred location for the crystal? If I would put it next to the chip, it would be in an area where all the decoupling for the USB power supplies is. If I would put it at the bottom side, it would require via's, in expense of the breakout of the digital signals. It seems there is no real pretty solution. I am used to crystal pins being at the edges of the chip, but unfortunately here this is not the case.
It is not advisable to connect both decap (of high frequency domains) and precision resistor GND points together. But if you have space constraints or other limitations you can do a star connection of these two nets to GND.
Preferred location for Crystal is on the top plane near the pins (restrict Crystal traces to 10mm). You can place decaps on the bottom plane under the chip. For better understanding take a look at SuperSpeed Explorer kit HW files.