I think it all depends on what you want from a guitar. The CEs have qualities that you just can't get in other models. Versus a Custom, you've got a bolt-on Maple neck, versus a SE/S2 same deal with the neck but you also get 5-way switching (in the case of the rotary).
Same goes for S2s, pick a S2 Mira Semi-hollow and you can't get that anywhere else in the PRS line (semi-hollow, all Hog).
The SEs rarely offer anything different from the other lines (except models like the Orianthi with the maple neck, ebony board) so really unless you have <$1000 and must have a brand new guitar, they're going to be second fiddle any day of the week. Second hand is a totally different story of course...
So apples vs oranges vs strawberries is my opinion! YMMV etc