I'd reboot both and have the rebooted UFO series dovetail into a Space 2099 series. UFO would depict the unification of Earth in the face of alien invasion (more like strafing or probing attacks as depicted in the original UFO). Space 2099 starts off with a human FTL drive accident/malfunction being responsible hurtling the Moon (populated by both Moonbase Alpha and a small human city called Lunagrad) into a distant region of the galaxy. During their attempts to return the Moon to Earth, the Lunar inhabitants encounter and resolve the antagonist situation caused by the aliens first encountered during the reboot of UFO.
I like the idea of UFO being in the format of For All Mankind and jumping a decade a season.
I like this idea.
Start with 1960s, or maybe "Today"
Series would be a bit more "Grounded" in real physics, less.. "Hippy" 1999 stories?
Show the start of the "Invasion" and the setting up of SHADO in the first season. Straker hitting up the UN for funds, going for a talent search, finding Foster, Freeman, Ellis, etc. Using current technology to attack the UFO's. Showing that current jets etc. are no match for the UFO's.
Maybe show Foster encountering one by chance, and destroying it, getting on Strakers radar and recruited as an ace pilot. Freeman as a General Hammond type of no nonsense, get it done attitude general. Ellis as a survivor of an alien abduction. finding other characters as the show progresses.
General Henderson as a competing agency like the NID and Maybourne from Stargate. that wants to lead the UFO charge instead of Straker.
Chunk of the series is just Straker going around, around mid season he gets the "Film Studio" office. The UFO invasion is not known to the public as of yet.
Ending with Straker and SHADO being formed and plans for a moon base, skydivers, SiD being finalized.
2nd season, time jump to show Shado as shown in the original series, moon base active, interceptors etc. Henderson part of the overseeing board of SHADO, at odds with Straker, but acknowledges strakers talent, but still adversary's on budget etc.
Story outlines like the original series, we're putting up a fight but the UFO's are still coming.
Film Studio base, Public still in the dark, but by end of the season, the secret comes out and the public knows.
Start showing the aliens side, by showing them on there planet, and ships, slowly showing the why's and hows of there invasion.
Ends with a large invasion force being stopped by SHADO.
3rd season, another time jump, Public knows, but are okay since SHADO has stopped the UFOs, any ship is destroyed by the moon base, which is now headed by General Henderson, and a now Major Elis, on approach by an automatic defense grid of satellites, drone interceptors, moon based lasers, so the aliens decide to incapacitate the moon. They cant destroy the moon as it would destroy the earth, so they use a large one way wormhole to relocate the moon, the aliens leave the destination open ended as they don't care where it ends up, just far away from Earth. This large wormhole used most of the power generation and capacitors of the whole fleets motherships, and due to the power, the moon is flung 120 light years away, and in the confusion on Earth, they invade.
This season would show the events on the moon and on Earth, the Earth wouldn't be destroyed by the moon leaving, but it wouldn't be pretty, some Tsunami's, and alot of confusion.
So by this season, its a duo story like Battlestar Galactica where they show SHADO on earth and the Moon getting there act together after being flung out. By this time we show that not all the aliens are onboard with the Invasion, and have Maya be an alien that helps the moonbase restore the FTL/wormhole drive so they can get back home, or atleast jump the moon from system to system using the moons power generation, and a capacitors They can't stop the moons direction or inherent velocity, so system stops are short.
Show SHADO and earth getting itself back together, but the aliens have committed to an all out invasion.
End the season with the aliens shown having gained control of Earth Orbit, and have landed and taken territory for there own bases, and the moon discovering a habitable planet, somewhat of a cliffhanger.
4th Season, no time jump, or a short one of like a year or 6 months, , the invasion on Earth is ongoing, with SHADO losing a war of attrition, aliens using small asteroids to bombard earth from Orbit.
Some moon citizens decide to settle the planet while the moon continues to the alien homeworld.
The moon through trial and error, or the alien takes them there, finds the alien homeworld. They discover that most have already left the planet with the invasion fleet, and all thats left is a handful ( 1000 or so) of "peaceful" aliens that would rather live on here than invade an inhabited planet. The water on the planet is pretty much gone, and the temperatures go above 140 degrees in the daylight.
Alpha takes the left behind aliens to the newly discovered habitable planet on there way back to Earth.
The moon arrives back in the Sol System, with Earth having fallen to the aliens, and they tell them about the habitable planet and offer to take them there if they leave Earth in peace.
Some hardliners say no, but some of the aliens we have been watching/following kill the hardliners, and then make a peaceful withdrawal from Earth.
Time jump 6 months, the aliens and moon colonists strive to co exist together on the new planet, the Earth is picking up the pieces, and the moon is slowly being nudged in to the proper orbit around the Earth.
Reason for Alien Invasion: Find a new home, there world is steadily heating up do to there sun slowly expanding into a red giant, this has been going on for millennia , there world developed life latter in there solar systems life cycle. ( have to have a plausible reason to invade!!)
Technologically about 300 years ahead of Earth ?, capable of slow FTL travel, short jumps then recharge there capacitors. ( 1,2 light year a month or so), this is more of a power generation problem, they could possibly go farther faster with better power generators. Robotic probes found Earth, and found that it is compatible, and it is the only planet in a 100 light year radius that has the right balance. Earth is about 20 light years away.
They have been warring over dwindling resources for 1000's of years, so there a war like race, and instead of coming peacefully they come to invade.
They find the human body compatible with there own bodies, so can reproduce with humans, with there genes being dominant and use them as body parts. Using the humans to repair themselves, and repopulate there dwindling species.
After the discovery of Earth, they send more robotic probes, and an advance scout force, with the UFO's and a larger mothership.
Over the years most of there people/fleet join in on the invasion.
When the Earth has fortified there system and no UFO's can make it to the planet, they use one of there mother ships to fling the moon out of the system to remove there defenses.
1999 was originally envisioned as a S2 of UFO, with an expanded moon base as the main area.
If i remember correctly, the UFO moonbase was NOT the only moon base on the moon, they defiantly had a Russian base, so maybe instead of just 2 cities, have Alpha and maybe a scattering of various other cities around the moon, Russian, Chinese, etc. or have alpha broke down into sections like the ISS, maybe even by that time some moon hotels for regular people, making it Alot more people on the moon instead of the 300+ on alpha in the 1999 series.
I would think they would be marginally self sufficient, growing own food, but needing certain items from earth.
EDIT: edited to include more stuff when I had a moment