Can we at the very least, say with reasonable certainty that a Star Trek starring Jeffrey Hunter would not have stayed on the air any longer than the Star Trek starring William Shatner did. Hunter died about a month after the third season ended. Then again, his death (of a cerebral hemorrhage) seems to have been related to an injury he sustained on-set while making a movie in Spain. If he'd had a steady job on Star Trek at the time, he might not have made that movie.

And with that being said, Hunter's Captain Pike arguably made for a very moody and dour character, in stark contrast to Shatner's more jovial and good-humored Captain Kirk. It might have made Pike a less pleasant character to spend time with, which could have made the show less popular long-term. As we saw him in the first pilot, could not possibly have interacted with the rest of that cast the way Kirk did with his. Whether that would have been worse or better, it's hard to say. It would definitely have been a different show.