I feel weird on this topic, because I have a hard time picking between the Jaguar and Jag-Stang without taking their musical usefulness into account.
The Jag-Stang lacks on the second bridge but makes up for it with it's insanely wild trem system (this thing beats a Floyd Rose IMHO for metal). I look more to that one for more "standard" metal tones and so fourth, and it's simpler switching which works better for me on the more frantic tunes where I don't have time to hit this switch, smack that one, and then roll a knob back. Basically, I consider it my pure rock-out guitar.
The Jaguar is a bit more arty of a guitar for me. I use it for the second bridge, very very very controlled pitch changes where pitch is utmost important. Also, it has a thinner sound that's unmistakably a Jaguar despite weather it's run clean or covered over in heaps of transistorized or tube generated gain. I usually run to this one when I need more control and a tighter sound overall, or if I need to play a really really fast part where the thinner sound helps give each note a beginning, middle, and an end.
As over analytical as this might sound, it's more of an in-the-moment-thing on which one I choose to play, basically, the point being, if it sounds right for the song, it's what I'll use.
