Both loaded they are the same price, but on the Subaru you get a Nav system and a couple other things I think. Subaru's low end model is 27K vs. 25.7K for the Scion so it is cheaper on the lower end.
It would be nice if they could bring the supra back. With the world pretty much catching up to them on reliablity they are going to have to stop making appliances like the Corolla or in a generation or 2 they are going to see companies like Hyuandi leave them in their wake.
I paid 24,800 for mine...4k cheaper than the Subaru at the time. Only diff is what I've already mentioned and the fact that the Subaru's had/have a lower production run so that jacked the prices up. The loaded Scions were not much different in price and they had nav with the bespoke audio system. On the initial runs the only real main difference was the push button start and climate control. Scion added that with the 10 series later on which, incidentally, they were charging the same price for as the Subaru.
You don't buy this car for luxury, it's a pure sports car built for handling...so paying out the nose for those things is insanity, IMHO. You were/are much better off getting a base Scion and pumping 4k in to tires (sorry, tyres!

) and whatever other performance upgrades (or aftermarket head units etc) you can as the car just gets better and better with that kind of love. This is strictly the North American market though, as there was even less of a difference between the two everywhere else in the world where it's under the Toyota name. Same car though...all built by Subaru in the same factory, despite what badge is on it.