Depends on which model deck you choose and options. If you plan on expanding the system and adding amps later, Pioneer has 4V preouts, some models with 6.5V. This sends more voltage to the amp inputs, resulting in cleaner sound and less background hiss.
As for adjustabiltiy in sound and eq settings (x-overs, Q , slope, etc.) you really have to step up in model and price with the Alpine to get the same adjustments as Pioneer offers on most of their HUs.
Both are great units. Personally I prefer Pioneer over Alpine and have Pioneer in all three of my vehicles. But the best thing to do is to probably head out to your local stereo shops and play around with their display units and see which one you like better.