"X-Men Origins" could be an alternate universe.

Leave it out? I saw that one in theaters but I keep forgetting it even exists.

I say you leave out The Last Stand as then Jean & Scott being alive at the end of DOFP makes more sense, the whole Raven/Charles relationship is still a mess but whatever, I mean there are still some large flaws imo such as the whole we created a mutant surpresant/power control serum in the 70's but we don't share that in the 00's with the terrified girl who cant even touch another person without risking their life, you also have the daft retconning of Cerebro and why Magneto's helmet can protect him, but yeah overall cut out TLS & Origins and things do work quite nicely.

Well cut out Dark Phoenix also as that is contradictive and daft also, but Logan I think isn't an AU but just a potential future from where DOFP left off, also you don't need TLS as The Wolverine establishes the key things you need to know that Jean is dead, I think Scott also is reaffirmed as dead maybe in the movie, Logan blames himself is what we can take away from the movie which how X2 ended would make sense, with Scott dying off screen a different way.

The 2 Angels thing then also fills in the how on certain easter eggs, like how did Stryker have ArchAngel design stuff? because it was Angel from Apocalypse not Angel from TLS, or there is only 1 Angel as without TLS we don't get the other dude and Archangel in the original timeline was a Stryker creation not an Apocalypse one and could have still been alive.