I honestly am kind of ticked they made the SE so nice. The pickups in the s2 are solid, but nowhere as good as these in the paul.
Even the mini goggles are amazing quality.
Just...wow. If it had a tremolo it would possibly be the best guitar design of all time (for flexibility).
If you have to be limited to a set number of guitars, would it not make sense to trade the S2 if its not up to the standard of the SE - at least from a functional and tonal preference to you. The S2 does use SE standard PU's but obviously are not based on the TCI pick-ups that Paul has designed. I don't know if the S2 you have offers split coils but I doubt it would offer the independent switching a Paul's guitar does. Another difference is the woods and I doubt the SE Pauls will be made of 1Piece Mahogany and maybe multiple pieces of Mahogany under the lovely veneer. Whether that makes a significant difference to you is something you may want to consider (or not).
At least with the Paul's, you will be getting the same bridge that PRS use on the Core version, and, if you wanted, you could upgrade the nut and tuners for relatively little expense. The birds look really nice and 'mother of toilet seat' that you often get. Point is, with little investment, you could improve the potential 'weak' links of the Pauls. Not to say that the nut and tuners are 'bad' but that they can be bettered and brought up in specs to rival the core Paul's in this area.
I would argue that even with a trem, a Paul's is not the most flexible guitar - certainly not compared to a PRS Special or the new MEv. It really depends on whether or not the Split coils are more usable than the tapped coils on a Special or even the 509. The Paul's, with a Trem, would be almost like a Custom 22-08 (not that this exists yet but the position of the neck PU and the 22frets would be more comparable than the Custom 24-08). Part of the reason I haven't really made a Paul's guitar as a 'priority' purchase is because I have a 594 which offers the same possible combinations (although I do prefer mini-toggles) and prefer the tune-o-matic adjustable bridge. The fact that PRS have seemed to crack the code to make 'split' Humbucker type PU's that sound more SC than thinner Humbucker - and not just for 408 sized PU's - the SE Pauls has regular sized PU's - could mean that Guitars, like the Custom 24-08, could have '85/15 TCI' PU's and improve the split coil sounds.
Anyway, that also depends on whether or not you think guitars like the Special or 509 are not as 'usable' as a Paul's guitar when you split the coils as both of these offer 'more' options for Pick-up choice and the trem too. In a lot of ways, I see the Pauls as a different sounding 594 - the Humbucking tones are more P90's in sound to my ear and of course you get the incredible single coil split sound too. I do think PRS have created something special with SE version and I must admit, I was tempted to add an SE Paul's and may well do in the future but right now I am making do (LOL) with my collection.
What ever you decide to do, I hope you have fun and decide which will give you more joy...