For example, I've heard D.C. Fontana's original script for "Encounter at Farpoint" was much better than the version filmed, which was rewritten by Roddenberry.
Erm, you heard incorrectly. It was decided to expand the script from a 90 min premiere to
two hours by Roddenberry adding the character of
Q, and the trial of humanity. Q is arguably the most popular recurring villain in TNG.
I felt it was odd he didn't want to include any of the alien species from TOS.
No, he argued in early press releases, and in the writers' room, that the galaxy was a really, really big place. Which it is. Since the intention, in "Farpoint", was to go beyond the tiny amount of explored space
on an extended mission, in a ship that didn't need to keep returning to Federation space, Roddenberry didn't want Starfleet running into familiar races in places where they shouldn't be yet. TOS had also had a very famous Vulcan, so GR suggested that race should only appear in cameos in the early TNG episodes.
VOY and ENT had ships that kept finding familiar races in unexpected places and many fans derided those stories.
The Bolians were created for no other reason than a script asking for an Andorian and Roddenberry not wanting one, so they made him this new species instead.
No, that was show-runner Rick Berman, reiterating Roddenberry's earlier suggestion to not keep revisiting old, familiar aliens. In addition, it was
Berman's belief that Andorians were "hokey, 60s sci-fi aliens", and he didn't change his mind until miniaturization of electronics had made moving antennae possible for Season One of ENT.
Roddenberry had no problem with Andorians. There were five of them in ST:TMP, although Fred Phillips redesigned the antennae as smaller, tapered, forehead tendril-like antennae.
On TNG, it was Rick Berman who told Tracy Tormé, "We don't do antennae on this show."
It seems they (Rick Berman and someone else who's name currently escapes me) practically had to smuggle the character of Worf past Roddenberry, because he was so much against using a Klingon on the show.
No, Worf was originally supposed to be little more than a cameo in "Farpoint", to show us that the Klingons and UFP were at peace. Michael Dorn turned out to be such a good actor that they hastily made the character a regular.