Having, and having had, way too many guitars, I have always felt the CEs to be the "louder, drunk uncle" (in a good way) version of the comparably- spec'd set-neck version. E.G. (haha) my 1991 CE24 definitely has more attitude than my 1991 CU24 with the same pickups. We're taking different neck AND body woods, in addition to neck attachment methods there.
I have one of the new CEs, and I love it. This is my only PRS with the 85/15s (although I have two McCartys with the 58/15s) and the CE definitely has some serious cojones when played against then back-to-back. But that's not apples to apples either, is it...
Of the two McCartys I have, pickups are identical, body woods are the same. One has a set mahogany neck. The other has a set flamed maple neck, and the bridge with the brass inserts. The maple-necked one definitely has a bit more presence; the hog-necked a bit more body.
This ain't night and day. We're talking (as Jack Gretz wisely put it) like maybe turning the treble knob from 7 to 8 difference. But it's noticeable.
I have really begun to prefer the feel of "less-finished" necks.