Well, the problems people have with t he Jag-Stang are not "wrong", it's just that they were design decisions that don't equate to a "more balanced" guitar like the Stratocaster, heck, it seems to me that most people a guitar has to be one of the big three (Les Paul, Tele, Strat), or a pointy metal guitar to compete, whigh is utter bull####.
The reason the Jag-Stang is bassy and dark sounding is because it's A.) Shorter Scaled, and B.) has a basswood body, which is a very airy, lightweight, not very dense tonewood, and very receptive to vibration, which helps the low end. Pair that with a bridge and tailpiece without a whole lot of mass (more warmth), and a humbucker in the bridge, and you are just asking for a really really low end heavy sound.
Basswood is a big part of the picture. It was used as a tonewood on Kramers, Charvels, Edward Van-Halen signature models (all of them), but the difference is, the Jag-Stang does not have a high metallic mass bass-sucker Floyd Rose trem on it, a longer and snappier 25.5" scale, and a figured maple top to stave off the added low frequencies of the humbucking pickups and basswood body. I think that was a huge mistake on Fender's part in making a "Grunge" guitar, as most of those Jaguars, Mustangs, and Jazzmasters were made of ash, alder, poplar, and at the bassiest, mahogany (some Mustangs were mahogany as a site I used to visit said and even had a picture of). A Jaguar or Mustang does not need a light body to sound warm as it's not competing with a snappy more midrangey toned 25.5" scale and a high mass counter-vibration stifling bridge. Another mistake was using 250K pots in a humbucker based guitar.
It's alltogether a great guitar, one of my favorites, but it just was badly put together for the market it was intended for from a more "mainstream" tonal-design standpoint, which I believe was more a result of Fender cashing in on Kurt Cobain's death than anything else. Also, some people are not going to like it for that fact alone, on some sides of guitar, there is a LOT of animosity against Kurt and Nirvana.
Anyway, to quit rambling about guitar geekery, different strokes for different folks, however, at the same time, a lot of these under-rated Fender guitars are pushed against by silly myths like the "bridge won't stay in tune" and "the bridge pickup sucks". There's only so much one can do with a guitar in 20 minutes in a guitar store. I consider the Jag-Stang my main "metal" guitar, it stays in tune at the trem, it's loud, it's bassy, that's why I play one, it does the job right, and out of a collection that includes a lot of stereotypical "metal" guitars, it seems the Jag-Stang is the one that always works.