i've a little more experience with the CIJ guitars than basses, but in my experience a lot of them are just under the average quality of the american made stuff. mainly in the electronics, but also for whatever reason, a lot of the tuners on CIJ's just don't seem to feel as sturdy or hold tune as well. All in all, the CIJ's i've played have all been good instruments, but I could detect some weaknesses.
For the record, the instruments i'm basing this on are: the older CIJ '72 tele's (the 250k pots they ship with are too dark for the pickups, it's pretty common to swap pots out ASAP for 500k), CIJ jazzmaster (needed shielding, pickup swap), aerodyne precision (decent bass, again cheap tuners), Geddy Lee (great bass all around), and the Jaguar bass (played 3 or 4, never found one that felt "right" to me).
Don't get me wrong, i still lust after japanese basses on a daily basis. Some seem to be fantastic, others seem to be just slightly inferior to the MIA's... what really sets them apart to me are the availability of cool color combinations that we never get here in the states. After all it's pretty easy to swap out some tuners or upgrade the pickups, but repainting a bass is a damn pain.