Well, it's a new year, which means you'll be filling out checks incorrectly. Also an excuse for people to start stuff over. But in this case, you'll be starting over something from decades ago: You're Gene Roddenberry, the pilot's been approved, and you've got a bigger budget than you originally expected: How'd you do Star Trek differently?
I've got a few ideas:
The Original Series:
1. Nerf the transporters. In this contrived setup, I've eliminated the original reason they existed: Budget. If Star Trek had more money, they would have done shuttle landings. Here's how I'd have the nerfed transporters work, if at all: It's primarily an emergency system. Repeated use on living things eventually leads to transporter psychosis like Barclay was worried about during bouts of hypochondria.
2. Rubber foreheads for the Klingons. The retcon just didn't sit well with me. Oh, and sort things out with the Trills ahead of time while we're at it.
3. Make a map in advance: Keep distances consistent, so you don't have the Enterprise jumping from one side of the galaxy to another in a manner that later embarrasses a certain Skipper, I mean female captain.
4. Episodes to kill: Spock's Brain and And the Children Shall Lead. Never happened. Really.
5. Episode to keep absolutely unaltered: The City at the Edge of Forever.
6. Fewer super-powered godlike aliens. Yeah, Kirk can talk his way past them. I don't watch Star Trek to see the crew flail helplessly for most of the episode.
7. Make Phase Two.
The Next Generation:
1. Keep the Borg insectine: The body snatching critters from that one episode that went gory were originally intended to be related to the Borg. Cyborg bugs would be cool.
2. Make the Ferengi proceed directly to comedic adversaries. They just didn't work out as real villains.
3. Take down the idealistic preachery down a few notches.
Deep Space Nine:
1. On the last episode, stick in the following scenes: Morn talks, Captain Boday makes an appearance, and Chief O'Brien discovers what a self-sealing stem bolt does.
I'll think of more, later.