I just recently went on a quest to buy my first PRS guitar... I read up about the SE the S2 because a full blown PRS was out of my price range. I liked the idea that the S2's body/neck was built here in the USA. I figured the electronics weren't as important and could be replaced if needed.
By the time I got around to actually holding a S2 and SE in my hands I came to the conclusion that the SE was indeed a lesser quality guitar. When playing the SE's there was a odd feel as my fingers moved up and down the neck, like the edges of the frets weren't flush with the edge of the neck, or something. The S2 felt much nicer along the neck. At that point I was actually also considering getting a Gibson SG standard and I played a few of those. I thought the lower end Gibson SG standards were similar in feel to the S2s that I had played... the Pots on the S2 and on the lower priced Gibsons felt very similar, that being somewhat cheap feeling...
So anyway, I had found this PRS S2 Custom 24 'Sapphire Smokeburst' at Guitar Center. I leaned it had PRS 57/08 pickups in it, and I had been reading about how coveted these pickups can be, etc... I got my heart REALLY interested getting one of these guitars that are exclusive to Guitar Center... but the price... $1600. Now for me, I don't really play much, I just have fun in my spare time, trying to play a little better then I do... $1600 is a lot of money for me to spend on a guitar. Long story shorter, is that if that Sapphire Smokeburst that I played had felt better, had better setup ( the action in the middle of the neck was high, assumed the neck needed adjustment ). I would have bought the dam thing on impulse.
However, I went on to find local store with a used 2006 PRS Standard 24, they they were asking $950 for. After playing this, there was no way I was going to pay $1600 for a S2, even if it did have 5708 pickups in it. ( well, I do still have some thoughts that the Sapphire Smokeburst S2 with 5708s has some collector type of value, but not enough to make it really worth it for me ).
Bottom line is... I'd advise seeing if you can find a used PRS, not a SE or S2. Play one, then go play a SE or S2... I bet you'll feel the difference.
Not really knocking a S2, or even a SE... but they are NOT of the same quality as a 100% made in USA PRS guitar. As in cars... You really are going to take a hit with resale value when buying a new guitar, used guitars can be a excellent value. It just requires a bit more shopping around, but with the internet, shopping for used isn't that bad. Just make sure you've actually seen/felt the guitar before buying. I would have a very hard time buying a guitar that I've never held in my hands, no matter what brand/model it is.