I completely agree with you. For me, that 'thing' is pretty elusive. I only have 2 guitars in the 'never sell' box. 1, is my AmStrat with a DG20 set up. Like Blackie for EC - It's the Strat that's right for me. And the other is - somewhat strangely - a late 70's or early 80's Memphis ripoff of a tele-deluxe. My bro got it broken for $5 bucks at a garage sale. I had it for 20 years and never did much more than somehow get one pickup to sort of work. Sky high action. Recently decided to take it apart - just as a project to learn on. Well, after replacing all the hardware and wiring and hooking up the pups correctly (which I discovered are vintage Bill Lawrence L500's - the real deal), shimming the brass nut, straightening the neck, etc I found out it's, well, perfect. Not the fretboard - could use a possible upgrade (thought that's it's own issue) but the sound is just exactly what I want. Better than any $5K Gibbie I've ever played.
I A/B'd all my guitars today (wanted to place the PRS's sound and figure out what I want). Anyway, found out that it does, indeed, have the worst sound - no harmonics or something - like it's compressed. As you suggested I'll play with the height but I don't think that's it (I had it professionally set up previously). However, there is something different about it and maybe this is true of PRS in general. It's just better made or something. I have 2 Epi LP's (prophecy GX (pretty great) actually, and plustop FX with the Floyd (project), a Taylor 414CE, and the others I mentioned and the S2 - I don't know, feels crafted.
After today (and your thoughtful note) I've decided to make the investment and see if it will sing. And I want to go pure PRS. So, now it's ordering and replacing the electronics, maybe getting a brass block for the Trem and then deciding which pups to get. I'm going for core pups - 57's, 85's or 59's. Now just have to figure out which of those is 'best.' I heard some 57,59 A/B on youtube and am leaning toward 57's. Don't know about the 85's except they seem loved. Would really love to get the Alex Lifeson PRS sound (I know he had a CE and a mountain of effects, but still...)
Sorry for the long post - kind of got away from me. Thanks so much for your thoughtful input. These forums are such a wonderful thing. Makes the internet seem worth it ;-)
Take care,
P