These are my theories about the timeline. Feel free to comment or question:
I think that the Logan/Creed mission we see in Vietnam is actualy 1975. Although the cease fire was established in 1973, the US army continued missions in southeast Asia untill April 1975. Mostly evacuation missions, but still. That explains the fact that Stryker doesn't recognize Logan in 1973, and why isn't Logan in the war... maybe he only went to the war as a last minute call 'cause Creed asked him, or something. Also, another thing, I don't recall to see anywhere saying how many years Logan worked for Team X, so the main story in Wolverine Origins could be in any year prior to 1986. If anyone could help in that matter, I'll appreciate.
Another thing they don't explain/neglected is why Professor X and Magneto are working together again when they went for Jean in 1986, and why is Professor X walking in that scene and in Wolverine Origins. Maybe they reconciled between 1973 (original timeline) and 1986, and afterwards became enemies again. As for the Professor X walking again, maybe he was on a lighter version of Beast's drug 'till it couldn't do the trick no more (also my theory why Beast is in human form in X2).
About Moira McTaggert: Yes, she's a geneticist in The Last Stand and a CIA operative in First Class. So what? People can change professions. Let's not forget that Beast is an engineer/doctor in First Class and X2, and the secretary of mutant affairs in The Last Stand.
Finaly, the thing that bugged me the most. Why are Angel and Psylocke in their 20's in 2006 (original timeline) and also the same age in the 1980's (revised timeline)? I've got another theory for that. When Logan "landed" in 1973, he didn't just changed the timeline 50 years forward, but also 50 years back, at least bits and pieces. That would explain why some characters changed their birthdates and origins background (like Jean, Cyclops, Colossus and Deadpool), and also why didn't Apocalypse rised in the original timeline but did so in the revised timeline. Like throwing a stone in the puddle: the ripples go to every direction, both forth and back.
Yes, it's a timeline with various flaws and gaps (mostly because the next writers don't respect the work of previous others) but, with a little imagination we can fill those gaps and correct those flaws ourselves. Sadly, we can only do it in our heads and foruns, and not in the actual movies.
There you go. Hope you liked it.