On anything other than pavement the prairie will usually lose, if it is in two wheel drive, due to excessive wheelspin.
Put her in 4x4 however and it aint even close. Also put the scram in 4x4 and it loses even worse. I know this for a fact because I regularly ride with a 500 scram and stock for stock we raced in all permutations possible.

 

I just bought a 1998 Scrambler 500 4x4. It has a Hot Seat performance kit which includes K&N Filter, jetting, clutching, and a pipe. I raced my buddy that has a new Prarie just got it broken in. We were side by side up until about 50-55 mph. After that he started to pull away from me. He hit 63 mph. The previous owner of my scrambler said it was clocked with a radar gun at 57mph. So the prarie speedometer is probably fairly accurate.

So a stock scrambler 500 would definetly lose to a stock prarie.

They are coming out with a lot of aftermarket parts for the prarie's. They are definitly a great machine, but they don't look as cool/sporty as a scrambler. Plus I spent about half the money for my used scrmbler that is in excellent condition to pretty much keep up with a machine that is 150cc larger. I am happy with my scrambler.