Any changes I'd make would be in season 1, "Justice" and "Angel One" easily could have been handled much better. Even "Code of Honor" has snippets of good ideas let down by misfire after misfire after "WTF casting" (more on that in a moment), and it's ironic that Roddenberry fired the casting guy given how racist "Justice" is (all guest cast are deliberately near-blond (or bleach wigged), haired blue eyed, oily greasy hornballs on a planet that somehow lacks STDs (and yet Riker didn't join in?!)... and not many whites - blue-eyed or otherwise - were as in much fervor over that, not even when the lady Edo (a diminutive of "Eden" and "Libido"?) calls Worf "the huge one" as if she's got a prejudice with size or something) - though keeping in mind "Justice"'s original story was a lot more developed than the rewrites that turned it into a brainless sexfest, not that there's anything wrong with
that I suppose...
But "Code" and "Justice" both show why TNG would, in later stories, show multiple skin colors. No matter how jaw-droppingly bad "Code" got, Jessie Lawrence Ferguson put in a strong and highly engaging performance that kept the story even watchable and from falling apart. Even the garbage that Patrick Stewart had to put out could have been a lot worse if someone else had been cast. Give them both real material and make the plot more than a rolling cliché with racist overtones (imagine if the guest cast were all white, would it make any real difference? Well, no... )
I'm a bit more reverent towards TNG than some of the other Treks since it was my introduction to Star Trek as a youngster. There's very little I'd change in the first three seasons except maybe those baggy redesigned uniforms that the men wore after "Booby Trap". Never liked them.
After Wesley left, there should have been a recurring character at the helm to interact with Data.
Worf and Troi should have never hooked up. She's Riker's woman.
A sequel to "Conspiracy" would have been nice.
Denise Crosby should not have come back as Tasha's half Romulan daughter.
There should have been more alien exploration, more danger in space, but less technobabble, and less soapy stories in the later seasons.
Definitely the last one!! Too much soap, the technobabble did get up there, and definitely more danger in space - which season 7 did try to steer the ship back into after the soapy 5th and 6th seasons. (Season 2 really had the exploration and danger things going for it, IMHO...) And Worf/Troi felt forced, but back then there was no idea of Worf going over to DS9 (much less marry Dax).
Data did need a foil and they couldn't just bring Geordi back. Imagine if Data and Geordi talked on the intercom with Picard looking exasperated all the time.
Though I like to believe Sela would have worked had she been written properly. By "Unification", she's so badly written that it's no wonder she magically disappears.
I would make Wesley a reoccuring character instead of a regular.
Troi's "powers" would be much weakened, to the point where they were a sometimes asset, but her real worth on the ship would be as counselor/morale and bridge officer.
Lose the aspect of the Enterprise being so close to Earth so often. Keep her far out on the fringes of known space for the most part.
Data would not get an emotion chip, his emotional awakening would come as part of his journey.
I would bring in Jellico as a replacement for Picard post-BOBW, and have Picard step down for an extended period. Play it as though Picard as a main character was gone for good. Spend some time with the crew and Jellico getting used to the style of each other before Picard's triumphant return.
I'm not the biggest fan of The Inner Light, but I would have loved a version without any of the "now" stuff. Just have Picard wake up to a new life and spend the entire episode treating it as though he's here to stay. Only at the very end reveal what really went on.
Wesley = quality over quantity and certainly we wouldn't get Wesley's idea of how thick a baseball bat isn't...
Troi's powers were rarely used effectively. "Farpoint" uses them just right, but week after week of seeing facial expressions so obvious that even an Aspie like me can also tell the captain what he already knows ("He's upset about something, captain"), etc... amazed that given how she's set up to have to deal with a thousand peoples' thoughts on the ship that when she's infiltrating Romulus ("Face of the Enemy") she doesn't pick up on anyone second guessing her performance as "the new crewmember who appeared out of nowhere" trope.)
Like all the TOS movies, any ship named "Enterprise" always seems to be hanging near Sol way too often.
The emotion chip was so inconsistently used in the movies... but, either which way, it's hard to write for a computer.
Jellico would be a bold move. Or promote Riker and have Shelby be the new #1 for a few episodes to keep the audience wondering if he survived the (extensive) Borg implants being removed. But Picard is irreplaceable either way, and Sir Patrick is a reason the show didn't get axed.
"The Inner Light" - nice ideas. Adds a bit more to the story. And the ending, get the townspeople to not be so limited to having the probe reaching out to only one special person and then self-destructing, leaving the special person telling this story that absolutely nobody is going to believe apart from the 3 people surrounding him in the episode, and even then...