Different Strokes for Different Folks I guess
So far the only thing on a bone stock Jag- Stang that might bother me would be the overly long Low E intonation screw that tends to work itself loose.
Most of the Jag-Stang's "problems" are a matter of opinion. The trem does'nt suck,It's just some people choose not to set it up in a way it WILL work, same goes for the bridge. After having my guitar about 2-3 hours, I had the Trem and bridge worked out. It's been running under that same setup for about 7-8 years now.
The pickups are also a case of taste. They might sound bad to one persons ears, but some might actually like them. I've played stock Jag-Stangs before and they don't sound bad, they just would'nt work for the high gain type Nirvana stuff, not enough bottom end. But they work fine for classic rock or something that uses lower gain and less bass.
On the subject of Kurt, he designed the guitar, but rest assured Fender was going to cut a few corners to get that thing out on time after his death. Fender IS a corporation just like any other out there, and while they have lines of guitars that are aimed towards the artist, they might have to make a choice between making the guitar more expensive (hurting it's chances to sell) by adding a TOM and SD pickups to it (at that time, Fender had a deal with DiMarzio as I recall reading, I think it was in the Frontline catalog).
Anyway, in my opinion, it's a great guitar anyways. No one guitar is the perfect end-all-be-all guitar, that's why guys like me own several different ones.