With the requirement that it still has to have aliens and explore at least one ship in space and be (reasonably) serious and not just a quickie easter egg encounter. No requirement on how much or how little violence or dialogue is needed in your new story.

I'd play down the wackier elements, like aliens causing the war or anything like that. I think I'd definitely keep certain elements in the DLC, like the uprising, but I think I'd try to introduce more of a rhyme and reason into the aliens plan. The main thing is understanding why the aliens are abducting and freezing humans.
It would instead be about labour. This alien group is taking humans and selling them/using them as labour back on their homeworld. Humans are physically superior to the Zetans (or whatever we wanna call them) so using them as labour makes sense. If the frozen humans were still there, I suppose they could just be test subjects, using people like Paulson for example to test how humans react to emotional stress, ie killing his family. The whole thing would be based around the alien overlords being corrupt and immoral.
I'd also like to introduce some friendly aliens. Maybe a sub group of anti-elitist aliens, or human sympathisers who also wish to topple the alien's cruel regime. Something to take away the feeling that all the aliens are just cliche evil space monsters. This would give the player some branching options that would include leading a human/zetan rebellion and stopping the evil alien overlord harvesting earth, liberating earth and allowing the good zetans to go home and fight the oppressors, or going total anarchist and flooding the ship with all the monstrous experiments, mutants and raiders the zetans have accumulated over the years. I could even see an evil ending that let the player become an ally to the evil Zetans, betraying both their own species and alien allies in exchange for vast riches that would improve his/her standing in the wastes vastly, whilst also allowing the aliens to continue their evil schemes.
I think Mothership Zeta is always gonna be difficult to execute well, as while Aliens function well as easter eggs, weird encounters, or random lore involving the Enclave or the BoS, dedicating an entire DLC to them, and creating this entire story around them is never going to work to everyone's favour. They're simply too far removed, and while I personally like the idea of these Zetans existing out there in the cosmos, building them up as a power that could wipe out the Earth, if they feel like it, is just too much. After all, if Mothership Zeta were canon, shouldn't an entire fleet of aliens be on their way right now to wipe out all life on earth as an act of retribution? It wouldn't be a leap, considering how vastly superior they are to the weak remnants of human society left on Earth.

It asks more questions than it answers.

I like options for talking rather than only fighting, so I might have set up a space-station-like environment, otherwise had the ship have more than one faction of aliens, good, bad, etc. A "living world" on the ship rather than mindless kill bots waiting for me to come down the hall and shoot them.
I think the ship needs to blow up in the end, though, because I really wanted to go show it to the brotherhood -- should have been able to, but couldn't. And that would ridiculously unbalance the main story of the fallout world.
And yeah, definitely remove any hints about the aliens causing the war.

It would have been awesome if Bethesda explored the idea behind the men in black. This is a really old conspiracy theory that is underutilized imo.

They could set it that one of the men in black contacts you or you discover a corpse from one of the men in black which progresses the story that would allow you to meet the group. You could probably add some stuff like aliens being kept by the organization or the fact that their existence is a secret that even the enclave does not even know of them then the story would transition to a world ending event via the alien mother ship where you help them destroy it.

You come across a traveler who sells you some Strange Chems. Once you take these strange chems, you are teleported as normal into the UFO with the same quests and characters.

The DLC is all just a dream to the Lone Wanderer in their hallucinations.

The aliens aren't little green men though, they're tough, bulky, and strong, almost like predators. The boss aliens look are have stealth boys and gatling alien blasters.

The rest of the DLC plays out exactly the same.

The DLC would start off in Rivet City's church. There you will talk to the priest asking if you believe in God creating the universe and shit. Afterwards, he will tip you off that a few days earlier, he saw something fall out of the sky thinking it's some sort of holy message. So you go to the crash site which is a big crater and raiders banging on the ufo. As you approach the ufo, the raiders bodies life up and explode and you too lift up as well only for you to black out.

DLC proceeds as usual. Shooty shooty the little green men.

At the end of the game, you discover that Sally was actually an alien that's been trapped in a human form for a long time (using a collar) because she was sabotaging the aliens plans of completely obliterating the planet. She then tells you that the main purpose of their arrival at Earth was to prevent the Great War from happening and make proper contact with humanity, but thanks to the vile crew mates that never happened and the entire crew witnessed global annihilation.

Going back to earth, she drops you off outside of Minefield and as a token of appreciation for freeing her, offers you a deal. You sell her pre-war items for alien energy cells for the weapons.

Well - the mod Mothership Zeta Crew does that for me at least. An entire new faction made out of former-Enclave soldiers traversing the stars under your direct command - and not to mention that all the people you found on board joined the faction as well apart from the cowboy and the slave trader.

And if this is all a dream of the main character, okay, of course, you don’t agree with strangers because they are an extraterrestrial race that experiments with people right up to the beginning of the era. Something like that, well, a lot of theory could be used with the ship, but take the fraternity but reveal the secret, and as we see in a foulout 4, they would erase the whole of Boston and Washington with the help of a death ray, and so well, if the enclave is well here, it’s the same thing, but not so bad, the MZK mod shows us everything is not bad, but others the targets could be traveling in the universe but this is nonsense though, and d ugih options I just do not like and have defaulted just hang out on the boat and drink and eat octopus, well, if other people cooperated it would be fun, you prischeltsev new captain and you have new plans for the experimentation.

Mothership Zeta Crew looks interesting. I haven't played fallout 3 since before New Vegas, so I only found out about it when it was brought up in relation to tale of two wastelands... sadly it sounds like MZC will never be fully converted for the next release