The Clipper cards used by BART are 90s technology that took so long to fully deploy that it was outdated by the time most people started using it. There was a brief window where if you were an early adopter it was better than what was available in many places (or not-so-brief compared to OMNY, which came along a decade later), but unsurprisingly the things designed later have mostly improved on it.

The killer feature that also causes most of the quirks is that it can be used to make payments fully offline without allowing double-spending of balance. This is of course mostly a killer feature for transit operators rather than users. OMNY solves the same problem by just accepting that it'll occasionally permit free rides.