Unfortunately you can't buy a new (2011) LP Studio Faded like mine new anymore. It has a polished solid maple plain top cap, mahogany neck, and rosewood fretboard. I quite like the Burstbucker Pro covered pickups in it. They sound really great with my Vox AC15c1 - right into the edge of breakup, no pedals. To my ear it is a really nice guitar and nice sounding, feeling, playing, etc.
Playing my new SE Tremonti Custom black/grey into the same amp, at the same exact settings, is a noticeably different sound, but also quite beautiful sounding.
This is obviously not the same comparison that you are making, because the Tremonti Custom has a maple wide/thin neck, etc., and is different from the 245 even though they have the same pickups. With the same pickups as my Santana SE, the Tremonti Custom sounds very different from the Santana.
Comparing an SE 245, I would say that the SE would be a great guitar. Never the less, if you could find a Gibson LP Studio similar to mine, it would also be a great guitar.
I agree that it is a shame that Gibson started substituting all sorts of design changes and different woods into the LP Studios, etc. Baked maple is evidently okay; I had a Gibson Tribute goldtop LP with it and didn't mind it - but the guitar had such major design problems and QC problems that I had to send it back. I bought a Fender MIM Telecaster Custom with the neck Wide Range humbucker in three tone sunburst and I really dig this guitar, plus it cost a lot less than the Gibson and had zero problems. I dig the WRHB's but I know some don't. Even though I think it is kind of an excuse when people explain things they can't explain as "personal preference", the only way I can explain why I dig the WRHB's is because of personal preference and I respect the opinion of those that don't like them. I think it is going to be the same kind of thing when comparing an SE 245 with an LP Studio. Personal preference. The equation can easily balance out when all the factors are taken into consideration - to your ear. Maybe so, maybe not.
I really dig my PRS SE guitars, but I'm not mono-minded about PRS guitars. I play a lot of different guitars and take things into consideration, then buy the one's I want - it could be one of a few different brands, for me, depending on where I'm trying to get to.
The 245 SE could be great, but I wouldn't discard the idea that there are not some really nice LP Studios out there just waiting to be grabbed. I'd say, just play them, check them out, and buy what you want. I am not a Gibson Corporate fan, but I dig some of the guitars. PRS is a way more ethical and player oriented corporation in my opinion; and personally, I would rather give PRS my money. At the same time there is no substitute for my very nice Gibsons, including my SG Standard (full pickguard, 490/498's, 2012'ish).
I guess I'm not indoctrinated enough, yet.