I reworked my first version to fit with universes. Some things may differ from the original information, but I am doing my utmost to make sure that most things fit together.
Earth-10005 (Original Timeline)
X-Men: First Class
X-Men Origins: Wolverine
X-Men
X2: X-Men United
X-Men: The Official Game
X-Men: The Last Stand
The Wolverine
The Gifted
X-Men: Days Of Future Past (Rouge Cut) (at the end just 1973 parts)
(New Timeline)
X-Men Origins: Wolverine (without Xavier physical appearance)
X-Men: Dark Phoenix
Deadpool
Deadpool 2 (without Logan references)
X-Men: Days Of Future Past (just bad 2023 parts)
Earth-17315 (Logan/Cable's Timeline)
X-Men First Class
X-Men: Days Of Future Past (1973 parts)
X-Men: Apocalypse
X-Men Origins: Wolverine (alternative)
X-Men
X2: X-Men United
X-Men: The Last Stand
The Wolverine
Deadpool
New Mutants
Logan
Earth-66250 (Peaceful Future)
X-Men First Class
X-Men: Days Of Future Past (1973 Parts)
X-Men: Apocalypse
X-Men Origins: Wolverine (alternative)
X-Men
X2: X-Men United
X-Men: The Last Stand
The Wolverine
Deadpool
Deadpool 2 Super Duper Cut
X-Men Days of Future Past (just good 2023 parts)
Earth-41633 (Deadpool Timeline)
X-Men Origins: Wolverine (alternative)
Deadpool
Deadpool 2 Super Duper Cut (Vanessa Lives timeline)
Deadpool 3
I like most of the films in this Franchise and I think they can give a lot if consistency issues are solved
Cable's future is designated Earth-66250. Earth-41633 is the timeline where the events of Deadpool 2 take place, not the ending. The Appendix explicitly calls the timeline where Deadpool kills Weapon XI a divergent timeline to Earth-10005, the original timeline.
I think I have an idea for you if you want to maintain the happy ending.
Earth-10005 - Original Timeline
Earth-66250 - Cable's Timeline
Earth-41633 - Deadpool 2/Peaceful ending
(James Mangold confirmed that Logan continues from the happy ending in DoFP but oh well...)
Earth-17315 - Logan/Venessa Lives Timeline
Actually, even if we accept that the happy ending is prior to Logan, the Deadpool 2 timeline could have led to any future where the characters have a happy ending. Just know that the version of Wolverine we see in Deadpool 3
will die. They've made it clear that they're not touching his death and Logan still takes place in 2029.
The Gifted has it's own Earth number now. Maybe you could argue it's the timeline at the beginning of Days of Future Past where the Sentinels attacked and Kitty sent them back in time so they could evacuate if you
really wanted to, but I think it's just standalone for now.
The Logan references in Deadpool 2 are because Wade has existential awareness of how his universe is fictional in Earth-1218 (our reality) and has knowledge of media that exists here. Because Logan came out in 2017, and Wade is in 2018, he is aware that it will happen in the future. Just like how in the comics he knows of future issues.
If an issue is the X-Mansion having young children in 2023 when mutants haven't been born since 2004, note that Xavier wants to open the school for both humans and mutants in X-Men: Apocalypse. Clearly he must have fulfilled that by 2023.
The original films are not connected to Logan. If you're trying to fit that in that deleted scene, understand that Xavier read Wolverine's mind and knows of events in both timelines. Plus, some details might be the same even if the events are totally different. That's why Wolverine has the sword from The Wolverine even though that movie isn't part of his new timeline.
I'm just going to say, there are no real continuity issues between First Class-Dark Phoenix, Deadpool 1-2, The New Mutants and Logan. Everything can be resolved without separating the films just because you can. You don't need to separate Dark Phoenix and Logan. Xavier returned to teaching sometime between Dark Phoenix and Deadpool and the school returned to its proper name.
