I have an S2 Studio and a SS, both great guitars, I would say the divide is two main questions - do you want a humbucker bridge pickup, and what kind of amp/setup are you going to be playing it through.
The strength of the Studio is that it can slide right into a rig set up for other PRS-type guitars and get great single coil tones, and a unique bridge humbucker tone, without really needing to tweak anything. If you're already playing amps/pedals that you like your PRS through, you'll probably immediately love the Studio with very little adjustment needed. Due to the all mahogany construction, the body gives more fatness in the low mids than an S-type guitar. The bridge humbucker is a fantastic pickup, more jangly and not as mid forward as PAF, and the best coil split I've used short of something like the 408 pickups or multi-tap 58/15's. As a whole, the Studio has an old school vibe, definitely not an 80's super Strat thing... kinda like if PRS had ever made a guitar for the Sears catalog, like an oddball Silvertone on steroids, 50's/60's pop jangle and great single coil sounds.
The SS, on the other hand, at least from my experience, is what I always want a Strat to be, but never is - different tonal profile, skinner sound in the low mids, but put it with the right amp and still a big thumping bass end, non-anemic midrange, more compressed and immediate note attack although can also be much smoother sounding than modern F guitars. The great sound you hear out of excellent late 50's/early 60's Strats, really, plus some. Just needs a different amp than the Studio, or at least one set up differently. The Studio can sound dull through an amp set up for a SS, and the SS can sound thin through an amp set up for the Studio (and other more traditional PRS guitars).
Price - given the craziness of the used market lately, and people realizing how good (and unfortunately rare) S2 Studios are, $1250 is on the high side but not unreasonable, I've seen them listed above what they sold for new. What's a good deal price, I would say around $900-1000 in good condition.
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