I think in retrospect it seems they overestimated the (relative) ease this would all come together. By the standards of the day Star Trek
was a significant departure from anything that had been done before for television. Perhaps not so much in quality but in sheer quantity. Everyone was learning on the fly that what served them before wasn't good enough anymore and they had to try new things to meet the new demand, the new standard. Established writers---even the SF ones---had to learn how to adapt to Star Trek's
format. The creators were taking it seriously and trying to get the idea across the show wasn't just silly escapism where pretty much anything goes and the show wasn't an anthology without episode-to-episode structure or consistency.
Today, and in no small thanks to TOS, there is (or should be) a much better understanding of what goes into a project like this. You've got to really plan in advance and try to minimize unforseen complications. You've got to hit the ground running. I doubt very few series today would get the grace period TNG enjoyed where it took more than a season for things to start to gel. Certainly on the post-production side we should have a much better handle on things then they did back then. And, in all fairness and as has been mentioned upthread, Star Trek
wasn't the only series to struggle. Mission: Impossible,
for one, was another high concept series with its own share of difficulties that were no end of headaches. It also wouldn't surprise me if Voyage To The Bottom Of The Sea
and Lost In Space
had their share of major migraines.
Things might have been different if Desilu hadn't had both shows (TOS and M:I) in concurrent production. If they'd had only one then it mightn't have been such a drain on resources. But they hit the jackpot (so to speak) in getting both series sold and only one would really last, possibly and partly because it had broader appeal and was more easily accessible for a general audience.