THIS IS AN OPINION.
YOU MAY HAVE A DIFFERENT ONE.
As a stereo installer for several years, and owner of a car stereo repair shop for a year (until I got a real job that paid real money), I would never replace a factory head unit without a good reason in a vehicle that was worth anything. The simple fact is that most factory units - in particular the upper end models, are most likely better than anything you can find aftermarket. They fit better, look better, and are repairable 10 years from now.
Not to mention you hurt the resale value of the car with the non-factory stuff.
If you want to change speakers, that is a different story but try to maintain the factory look unless you plan to market your car to 16 year old boy racers.
The downside to the factory setup would be in special features like an i-pod interface. There are ways around this though and should be looked at before you downgrade to an aftermarket head unit.
btw, the factory head unit in my 1998 Explorer already IS made by Pioneer.
My 1991 Audi has a Blaupunkt/Bose system. In both cases it would take some serious money to build an aftermarket system that out performed them - unless all you were after was lots of noise.