There was absolutely a different feel to the series in the final season.
Definitely a shakeup. The show was renewed, of course, after the write-in, but Roddenberry left in a huff because season 3 was originally to have moved back to Monday (but didn't, thanks to the creator of "Laugh-In" getting in a huff over what was promised to Roddenberry... and chances are, "Laugh-In" wasn't as expensive to make, and was seen as new, whereas TOS was now seen as "old hat". As Chekov was created to appeal to younger-adult audiences, the Friday night slot has a counterintuitive effect as the young adults are too busy getting busy elsewhere...)
The music was frequently darker.
A terrific change. the occasional change in style can be important and TOS had so much reused music that new stuff had to be scored. A lot of it is quite good, IMHO.
The season embraced more high concept stories,
Of which many work, even the flawed ones, especially when the script feels like it's trying.
lost the soft focus for the ladies,
A big change. The show's level of sexism started to drop as a result. Or, rather, at the moment, in recollecting TOS, the worst sexist stuff came in season two. Not saying season three got rid of it entirely, but would seasons one or two have Vanna as a miner, for example? (Then again, this same story has Spock - once reticent to discuss his sex life to anyone in even a high-level summarization and in a carefully crafted story, "Amok Time" - now has him so freely discussing the issue as if it's no different to how he prepares morning breakfast as small talk. I suppose the idea is to try to clue in new viewers* on character background in lieu of nonexistent home video, and audiences having to listen to Droxine whine incessantly about why Spock is avoiding the issue (just as much as when little Missy and Tommy keep whining "Are we there yet!!!" during the vacation drive and all) would not be a great use of 5 minutes of screentime... still could have been handled better, if even needed at all. We know Spock, like all Vulcans or partial Vulcans, control emotions through (what would be named as "Kolinahr") and other extreme rituals, which were hinted at in various stories, of which "Plato's Stepchildren" is one of the more recent entries. )
* Which likely didn't exist. By 1969, only established fans kept watching the show that would sit through anything, especially considering the "creative, detail-driven fanfic" created in the early-70s involving Spock's parts reminds of how tuned-in many devout fans were at the time. Which shouldn't be poked fun at too much, since at least there was some creativity applied and just didn't have the same parts and processes that bog-standard humans have. I wonder how many of fans in this area become biologists in real life?
and about 90% of the banter was gone from the series.
Some of it was missed, but it's also a step up. Chekov's act was so overdone and was more as (unintentionally?) backhanded insults, as well as character-stifling.
The show was also in the 10pm timeslot, so there was a bit of an increase in the danger and brutality.
Mostly a plus, especially as the show was deemed "adult sci-fi")**. Showing space can be a dangerous place. It's an easy trick to up the dramatic stakes, and more often than not, the drama was confined to the characters as small to mid-scale. No impending big galactic catastrophe as sweeps week threat fodder.
** Apart from, arguably, "Where the Children Shall Lead" (the worst episode ever)
Without Roddenberry, Fontana and people like Coon or Lucas passing the scripts around for rewrites, the identity of the series changed. It reflected the styles of Fred Freiberger and, probably more so, Arthur Singer. And from Whom Gods Destroy to the end of the series, it was just those two guys rewriting scripts from mostly freelancing newcomers to Star Trek.
Aye. Coon and Fontana definitely were as much the heart of the show as Roddenberry... but they too did story fixes and co-wrote teleplays for newcomers (e.g. "A Piece of the Action") to get iffy scripts up to something almost Startrekkish.
From what I remember reading, had there been a fourth season, Margaret Armen would have become the official script editor. That would have been cool.
Season 3 was a shake-up, but looking at "Whom Gods Destroy" onward, there are a few messes and a few missed opportunities. But none that are uninteresting. Which reminds, even "The Savage Curtain" (the weakest of the bunch in terms of plot ideas) ties into "Day of the Dove" in an interesting way. Note a comment that Kirk says in "Dove" about learning about the Federation, to Kirk and Spock recognizing "Kahless" to how Kahless is revered and expanded on by Worf and others in TNG... likely unintentional, of course, especially as nobody in 1969 would have ever have guessed that a TNG would have meant anything
other than "Tender Nummy Guppies" for all anyone might know.
So, yeah, it's not really the same show. The characters are there, the sets, and most of the production crew, but the story minds are different.
It's a mess, but it also feels like they were trying to get out of what felt like a rut at times. Even "That Which Survives" had to do a lot of plot juggling with the budget cuts, since the defense system should easily produce more than one killer security sentry with as the system is otherwise inefficient. Cool use of platform to have all the actors lose their balance on at the start, though. That said, Spock's character was a tad off the mark in this one as well, used mostly for comic/lampooned effect as well.