Here's my personal take on this one...
I don't think Kurt truly hated the Jag-Stang so much as Fender did not produce it to the specifications he wanted because of a mixture of OEM parts sources Fender had an agreement with at the time, and certain things involving hardware that have since been resolved. Those and Fender had more concern in making a "mainstream palatable" guitar (ie. balancing the body through the odd reshaping for example). While Kurt may have intended the Jag-Stang as a one off (maybe not), maybe Fender was already thinking of a production model well before Kurt died.
If it had been to Kurt's specs, it would have likely been contoured, had a Seymour Duncan J.B. in the bridge and hot-rail in the neck, a Tune-O-Matic bridge with Jaguar tailpiece, and simplified switching, and his 3X3 headstock idea.
Here's why those maybe would not have happened at the time....
- No Contouring and oddly skinny waist due to "body balance" issues for the cork-sniffin vintage/boutique guitar snobs so they don't turn their noses up at it when it gets magazine reviews
- No S.D. pickups because at the time, Fender had a deal with DiMarzio. The HM Strats, Ritchie Sambora, Yngwie Malmsteen, and a lot of other guitars Fender made at the time were using DiMarzio or DiMarzio designed pickups, whom are a major competitor of Seymour Duncan.
- No Tune-O-Matic because, at the time, Fender was still trying to keep to their original image and original hardware, plus I think Gibson had some kind of odd trademark at the time on the Tune-O-Matic design that would have prevented "copycats" like the Adjust-O-Matic bridge at the time.
- No Jaguar tailpiece because someone @ Fender thought it would make the guitar look "funny" at the time.
- No 3X3 headstock because, Fender would want their guitar to be easily identifiable as a FENDER with that FenderHeadstock on it
When Kurt Got the guitar, Ernie Bailey would switch the stock bridge out for a Tune-O-Matic, flip the tailpiece, and put in a SD J.B. Humbucker where the H3 would go. Then it would get sent back to Fender either that way, or possibly, maybe to keep from losing the deal or confusing the designers, they switched it back when the prototype went back to Fender for adjustments to the design.
One thing that always threw me for a loop was the Frontline interview. Sounds almost like someone did a write in for Kurt in the final paragraph...especially the "It's perfect for me to attach my name to the Jag-Stang, in that I'm the anti-guitar hero - I can barely play the things myself". I remembered reading somewhere else Kurt did not want to put his name on the guitar anywhere, or did not want it as a signature model/have his name for preconceived notions attached to it.