Of the basses I've owned, the biggest disappointment was probably a Ken Smith BT5-EG. I received it with one of the circuit boards in the preamp broken off the pots, and figured it wouldn't work at all, but for some reason, with the bass in passive mode and the pickups in series, it sounded like the voice of God. I got the parts to fix it (after a rather condescending exchange with KS), and after the repair, it sounded much worse-very thin, compressed, and dull. Perhaps it was just the voicing of the preamp, but it definitely wasn't my thing.
Second biggest disappointment was a '75 Alembic Series I. While it was well-built and played fantastically well, the bridge was a crude design when it was new, and after 30 years of wear, the saddles rattled on their adjustment screws and were constantly shifting, and there wasn't enough break angle over the saddles to keep the strings firmly anchored in the slots. Worst of all, the adjustment screws for the saddles were permanently attached (the nuts holding them in the bridge were peened on), so there was no way to take it apart without destroying it. My luthier fixed it well enough, but I got tired of it and traded it not long after. While modern Alembics are wonderful, you could tell that they were still learning when mine was built.