I see that there's a lot of love for the standard version, and that's what gets my vote, as it's the only one that doesn't leave me with thoughts of "I wish it had" or "Instead, it should", etc.
I can definitely say that my least favourite of the bunch is the JPX, for a couple of reasons. First and foremost, I don't like chambered-bodied guitars. I figure they should either be totally solid, thinline semi-hollow bodied, or full-depth hollow body...chambering an otherwise solid body seems weird to me. Secondly, the 5-position lever pickup selector switch doesn't suit the JP series, as every one of John's guitars have always used the 3-position toggle switch, even the Silhouette Bass Guitars that he's used. Third, the black hardware just doesn't look nearly as nice to me as the chrome hardware. Fourth, I've never seen any evidence of John Petrucci himself employing this particular model, whether it be in a live video, instructional video, nor do I know if he's ever actually used it on any studio recordings. Finally, the pairing of the alder body and the ebony fingerboard, both of which woods possess a high resonant frequency, seem like they would combine to produce an incredibly bright guitar tone.
As for the JPXI, the aforementioned undesirable (to me) pairing of alder and ebony is present on this model, that, and, the only body colour option of onyx (plain in my eyes) is limiting.
As for the JPXIII, I like the woods and hardware being used, however, the active on-board preamp seems scary, however, as John Petrucci has been using this model on the upcoming Dream Theater album, upon hearing the tone of these new pickups and the booster circuit, I might change my opinion. Like the Onyx finish of the JPXI, the silver finish is a little plain to me.
The BFR model is sweet for obvious reasons, however, out of all the non-standard models, my favourite would be the JPXII, as I enjoy the pairing of the basswood body and the ebony fingerboard, and the 20" fingerboard radius. The Cherry Sugar finish is nice online, but in person, it's heavenly.
One strike against all of the non-standard models (in my eyes) is the lack of options for the features. For example, I'd love to get a JPXII, but without the piezo bridge and with standard dot inlays.
Now, don't get me wrong, all of the Music Man models are top-notch, and I didn't write any of this to put any of these models down by any means, these are just my opinions. No matter what, the entire EBMM JP lineup is indisputably recognizable as a group of well-made, easy to play, great sounding fine instruments, and I'm sure there's something for everyone (although I wish they would allow customization of the feature appointments on the BFR, JPX, JPXI, JPXII and JPXIII models!)