It was one of the ones which nearly got away. Originally, Capcom USA was not going to release Mega Man X3 or its Classic series stablemate, Mega Man 7. The game came during the console's twilight years, which is evident in the ports made to the next generation platforms Sony PlayStation and SEGA Saturn, and the Western branch of the company apparently didn't feel there was a market for it. But, due to demand (interestingly enough, in an age before internet usage was commonplace), they eventually conceded and released both, albeit in limited quantities.
GameSpite takes a look back at Mega Man X3, positing that the series had seemed to reach a state of creative stagnation more quickly than the original series. Perhaps this, combined with being released so late in the Super NES's life cycle, is what led to Capcom USA's initial way of thinking?
Of course, as we now know, it would only be another year before Capcom would expand on one of Mega Man X3's more unique (for Mega Man, anyway) features, leading to something of a new lease on life for the series.