I had this situation twice: a Gibson Thundebird, and a Rickenbacker 4003.
I've always liked Thunderbirds because of John Entwistle, and I immediately fell in love with the Gibson neck as soon as I tried it in the shop. But I've noticed that it sounded a bit dark right in the beginning, and I put Rotosound 66s and a pair of alnico Chinabuckers in it which both helped. Later I discovered that modern Gibson Birds have pickups too close to the neck, so I sold it and bought an Epiphone VP (my main bass now). Its neck is a bit thicker but man is it a tone machine.
I bought the 2008 Rickenbacker for a bright, Chris Squire sound capable of stereo pickup routing. It was very problematic: high nut, uneven frets, buzzing bridge, stock pickups too dark, truss rods on the verge of breaking. I replaced them all with a brass nut, Toaster neck pickup, and Hipshot bridge, and it's a solid player now with an amazing neck (albeit damaged fretboard lacquer due to refret). Now the only things stock about it is probably the wood, tuners, scratchplate, and bridge pickup!
I'm not intending to perform such life-saving surgeries on other basses, though. Some basses I just love it stock (the VP Thunderbird, my Höfner Ignition), some basses I just sold it for a better option (my previous SG and Viola ass), some basses I bought as a mod platform (my Steinberger copy, my former Tokai). For a mod platform I know where I'm gonna end up, and mostly end up happy with the result.