I wouldnt say out of the box I prefer SE's over cores, but once I do the whole refit job on an SE, which includes setup, nut change, replacing saddles on trem equipped models, swap out input jack, and put new pickups in there, the difference is almost nil at that point. Now of course all that is gonna be some cheddar for those that dont want to do it themselves or don't know how, but even if you paid for all that, its still a bargain. I mean....look at it this way:
A core PRS is gonna be 4k new. I can buy a new SE for...let's say the Paul's model at 1k. I invest say...$500 (which is what I put into my PG SE) in all the items I want to get it as close to a core as I can (hardware, tuners, fret refinish/polish, jack installation, pickups). I will eventually get 95% the guitar for about 37% the price.
In the immortal words of that dude from Robocop, "I'll buy that for a dollar".