It all comes down to portability, XM NavTraffic, and ease of use. The Pioneer system is easy to use, especially while driving. I know the Nuvi is as well, but then GPS unit is in the dash, always available, and controls everything.
You will probably get newer maps with the Nuvi, as it seems that Pioneer only updates their maps about once a year, normally when a new headunit comes out.
I have used the Nuvi before, and I like the Pioneer map system better, especially with POI and ease of finding things on the map. Also watching DVDs (err. letting your passengers watch DVDs) while driving, and having everything at the touch of your fingers, without having wires dragging across your dash.
Also not getting pulled over in those states that don't allow radar detectors when they see the portable GPS on your dash (happened to me once).
The nice thing about the Nuvi, as with all portable GPS systems is just that, they are portable, so no matter what car you go in to, you have a GPS system with you.
I have the Pioneer AVIC-N3 in my car, and I have a bluetooth GPS module with Pocket PC software (I have a Pocket PC Phone), and use the GPS with my phone when I don't have my car to guide me.
So it all comes down to do you want indash GPS with POI search, telephone search, easy to use interface, DVD Playback, iPod Connection (possible), AUX inputs, CD Changer input control (possible), XM radio (possible), XM NavTraffic (possible and in areas where it is supported), or do you want portability?