The '07 PMR is a great paintball marker. It is consistent and reliable. The marker performs and shoots ropes out of the box. If you have the skills, you will be able to keep up with the more expensive, "high-end" markers.
The one upgrade that I would strongly recommend is replacing the composite back cap with an aluminum one. Some owners have a tendency of stripping out the threads when they are taking down and reassembling the marker for maintenance. Warrior Paintball (ANS Gear) is only $10 or you can spend up to $30 for other brands.
Another upgrade to consider is a clamping or quick-lock type feedneck. The stock feedneck works, but to adjust the tension, you need to use a 5/32" allen key.
All other upgrades are preference.
The stock board works great and is programmable. Unless you have money burning a hole in your pocket, there is no need to replace it. You can configure the following settings:
Trigger Sensitivity
Dwell
Rate of Fire
Fire Mode (semi-auto, PSP, and Millennium)
The default ROF is factory set at 20 bps. You can program the ROF for 10 bps to 30 bps (maximum.)
http://forums.matrixowner.com/ is a great resource for Dye/Proto owners.