I've owned a couple PJ5s, a Metro and NYC. I would usually favor the P 99% of the time (Love that sound!) maybe on a couple of tunes I would use just the J, but I did not like the sound that was produced with both pickups on... not an "inherent flaw", but just my opinion...YMMV.
It just sounded out of phase to me, maybe because the J has it's focal point in a straight line across the strings and the P has it's focal points in two different spots? Maybe Lee Sklar was on to something when he used Two P pickups?
I'm an old dude who dove into the modding craze in the late 70's and 80's. I was a P-bass guy who converted a number of basses to PJ, some active and some passive. IMO the only "inherent flaw" is in expectations: a PJ with both pickups dimed will never sound like a Jazz bass with both pickups dimed, especially on the D and G strings. All that means is that PJ is different from JJ -- better/worse is a judgment call.
To be fair there were other PJ complications such as pickup output levels, and the fact that a single-coil bridge J will never wind up in a humbucking configuration -- but these are complications, not flaws. Companies such as DiMarzio, Duncan, EMG, bartolini caught up with the modding craze and released balanced PJ sets, usually with humbucking J pickups.
I actually built a tribute to Leland Sklar's Frankenstein bass with two EMG P-pickups setup V-V-T. It's got a great tone... kind of like a J-ish P bass. It works like a Jazz bass, where you get a more scooped tone with both pickups full-up, and if you favor one or the other you get more of those neck or bridge qualities. I tend to use both full on, or with a little off of the neck pickup. No noise of course
With my Sadowsky P-soap 5-string, I favor the P 99% of the time. I had a NYC PJ for a few years, which I adored, and I did the same thing with that one. It's a great P-tone. Sometimes, I would use both pickups full on but I find the D and G strings sound a bit nasally for my preference. Not like a Jazz bass. I have been experimenting with pickup height though, and welcome any suggestions for that. I use Roger's setup tips as well and love them.
As an aside, I recently found an '85 Yamaha BB 3000 bass with a single coil at the bridge. It sounds great and has surprisingly little hum with the single coil in the mix. That bass is V-V-T and has Les Paul-type knobs with numbers and a clear "1-10". I've been experimenting with adding a little J into the P-bass tone and find that a little goes a long way. Now, with my Sadowsky P-soap I'm experimenting with the same thing. So I guess I've learned that 50/50 is not the only way to use a PJ!
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