Some of my thoughts:
-Get rid of "Code of Honor." Rework most of the first season, except for "Heart of Glory", "Conspiracy," and the Q parts.
HoG is solid, though I'd find a better time to explore Geordi's VISOR transmitter than during a mission of extreme urgency where the ship they beam onto might explode at any given minute, so what do they all do - apart from standing there blabbering about how slick it is... the scene in of itself is still good, but juxtaposed against the main plot and the urgency of the rescue, it still doesn't fit.
Roddenberry could be hit or miss with his ideas... Q was not a miss.
-Revisit the "Conspiracy" parasites, and I would've liked to have seen Tryla Scott back as well.
The actress for Tryla had a charisma and a strong character personality. Would loved to have seen more of her; she'd be strong enough for a spinoff as lead as well.
A sequel never did get made for these space crawdads, which were to be revealed as an agent of the Borg - before the writers' strike clobbered the ideas for an insect species, hence the (less expensive) cybernetic gestalt instead. The galactic prawn wouldn't have been as lasting...
-Revisit the Devidians and Schism aliens.
Definitely Devidians.
-No families on starships.
But we'd miss out on that kid, little Harry "Sheldon" Cooper, whining about taking advanced calculus at ate 14!
-I'm iffy about getting rid of Picard after "Best of Both Worlds". I like the idea of Captain Riker and Commander Shelby. Perhaps I would've settled on having Picard get treatment for like the fourth season or half of it, while we got Captain Riker, and then have Picard come back. That might create some Kirk-Decker like tension between the men. I also like the idea I've read here of Admiral Picard.
A three-parter BOBW would have allowed time to explore that idea, if not longer. I loathe "Family" after BOBW2, as that sort of generic soap opera can be found in "The Waltons". A lot of early season 4 is a condensed shtick version where a crewmember has some traumatizing thing happen - Data meets daddy and Lore shows up, Beverly is sent to a shrinking domain, let's get Picard stabbed by that kid from "Our House" (read: "The Waltons, on valium"). That said, BOBW2 is surprisingly robust, especially with the need to deliver a script quickly.
-Replace Will Riker with Thomas Riker. I think a little shake up would've been nice. I've liked the ideas I've seen over the years about that change. Will could've gone on to captain another ship and Thomas could've stayed on the Enterprise-D, rekindled his romance with Troi. Data could've moved up to XO which would've strengthened the Picard/Data dynamic from the movies, and that exists in ST: Picard. Tom Riker as part of the crew also could've led to some nice character moments for the crew as they have to readjust to him.
It'd allow the actor to stay, which would be a plus. Never cared for how Thomas was handled in DS9.
-Start Geordi off in engineering from jump. He's like the youngest engineering chief in Starfleet. I would've had his family on the series much sooner. And he wouldn't be as unlucky with the ladies.
To be a fly on the wall; he spends a lot of time down there to begin with, despite the wordless gag about "blind man driving the ship". Add in the merry go round of chief engineers, all of which make a log cabin's primary constituent more exciting by comparison...
-Keep Sonya Gomez around longer. Maybe go forward with the idea of her and Geordi becoming romantically involved.
There wasn't much screen chemistry there in any form. Maybe more episodes would have improved, but Gomez feels like another example of "The Cousin Oliver Trope" where they bring in a new castmember to boost ratings.
-Would've had Troi in a standard uniform from jump. Made her the diplomatic/first contact officer. I don't see why a ship's counselor needed to be on the bridge, despite Troi's empathic abilities.
^^these
-I didn't mind the idea of Leslie Crusher. But in any event, I would've made the character a bit older, a cadet or ensign, and they would hold a grudge against Picard for Jack Crusher's death.
^^this
-I like the idea of an Andorian on the ship. As ship's doctor would've worked for me as well. I was fine with Gates McFadden in the doctor role and hoped she wouldn't mind blue makeup.
Hmmm, Dr Pulaski from Andoria...
-Have Tomalak as a recurring villain. If they couldn't get him, then create a new Romulan recurring villain. Fleshed out Romulan culture like they fleshed out Klingon culture. And I would've borrowed a lot from the Diane Duanne books.
^^this
Or give the role to Sela, with better dialogue. Her season 4 finale/5 opener treats her decently enough, but "Unification" treats her like a looney tunes character.
-I would've still had Tasha leave the show, with the crew presuming she was dead, but really she had been captured by the Romulans and brainwashed into believing she was "Sela". I think the first season finale "The Neutral Zone" with the return of the Romulans and the barest hint of the Borg would've been the best place for her "death."
Interesting.
-Had a Mirror Universe episode or two.
I'm glad TNG didn't go there, yet I'm surprised they didn't think of it by season 7 - or 8 had it been commissioned, but too much of 6 and 7 were so coasting on fumes, especially when writers went to give the A-grade good stuff to DS9.
-Made "I, Borg" the last Borg episode for TNG. I like the idea I've seen of the Borg not having a queen. It worked for First Contact, and the actresses who have played the queen have all been good, but I was more chilled by the impersonal force of nature the Borg were in "Q Who" and "Best of Both Worlds."
"Descent" grew on me, at least for the Borg splinter faction being psychotic sociopaths. The rest of the story is snoozeville at best, complete with awful acting.
Ditto for not having a Queen, the purer gestalt nature where they're all capable to work out issues and come to a decision without needing a generic leader figure to do it for them.
-Made "Best of Both Worlds" a three-parter, with the middle part focused on the Battle of Wolf 359.
With the budget, wouldn't that be hard to do?
-In earlier seasons, mentioned the wars with the Tzenkethi and Cardassians.
Maybe throw in the Tarellians; "Haven" lays some pretty dark groundwork, but the episode spends more time showcasing "80s hair" than anything else. Riker and Troi were still too new and the relationship stuff felt a bit tacked on that early into the show.
-I also liked the idea of developing more of the races introduced on TNG more, but also some TOS races that weren't explored much. The special effects might not have been there but it would've been nice to see a Caitian or Edoan. It would've been easy to bring the Efrosians, Deltans, and other TOS movie species back, if nothing else in background roles. There were quite a few The Motion Picture species that could've been fleshed out.
^^this
-A Stargazer flashback episode.
Other than "The Battle", which is one of TNG's earliest examples of a robust story. Or what could be one given the behind the scenes issues. The second near-classic after WNOHGB, IMHO... maybe as a later episode, seasons 6 and 7 needed better ideas to tinker with. Assuming Picard stayed, which he did...