The character of Number One was a bit ahead of her time, and Roddenberry had to cave to network "sensibilities" and give her up (maybe if he'd offered to have put her in a cat suit, things would've been different).
But TOS was able to work quite a few strong female characters into important positions in episodes, even if some of them were wearing mini-skirts (or even less).
As far as major characters on other TV shows go, where are the strong female or minority leads? How is Trek failing in this area compared to other shows where the lead could've been male or female but was male? Hell, why wasn't Greg House made Marge House?
Just within Trek, two subtle but important things were done that you don't see often on TV. A woman, Kate Mulgrew, was the lead in VOY, and an African-American, Avery Brooks, was the lead in DS9. Regarding the latter, there have not been too many shows on TV (I seriously can't think of any now other than I Spy and Room 222, both from the 1960s) that had an African-American actor as the lead of a predominantly white cast.
Trek could've done better. It could've done a hell of a lot worse.