To be honest, the continuity in the series has never been great
I see this on a lot of forums but don't follow.
The only issues I can agree are problematic are Moira, Angel, Psylocke & Trask from X3 being used in
First Class,
Days of Future Past and
X-Men: Apocalypse. Clearly Singer wanted to reboot those characters and I'm glad he did. Trask was essential to DOFP & Munn's Psylocke was far superior to the two-second Psylocke we saw in X3.
There's really nothing else that doesn't fit.
Timeline A
-4000 B.C., a teenage En Sabah Nur builds the pyramids.
-3980 B.C., En Sabah Nur, now an adult, bonds with the Apocalypse entity but is buried underground in a comatose state.
-1829, Victor Logan is born in Canada.
-1832, James Howlett/Logan is born in Canada.
-1845, Victor and James flee Canada to America.
-1861, The Logan Bros. fight in the American Civil War
-1918, The Logan Bros. fight in WWI
-1931, Erik Lehnsherr is born.
-1933, Charles Xavier is born.
-1933, Raven Darkholme is born.
-1944, The Logan Bros. fight in WWII; Erik Lehnsherr is placed in a Nazi concentration camp where he meets Sebastian Shaw; Charles Xavier's family adopts Raven Darkholme.
-1945, Wolverine is captured by the Japanese. Survives bombing of Nagasaki.
-1962, events of
X-Men: First Class.
-1963, Magneto is arrested for the assassination of JFK.
-1965, Wolverine and Sabretooth fight in the Vietnam War.
-1973, Wolverine works for the mob while on leave in NYC; Wolverine then returns to Vietnam where he and Sabretooth are executed & subsequently meet Stryker; Mystique kills Bolivar Trask in France.
-1979, most of the events from
X-Men Origins as Wolverine volunteers for the adamantium bonding process, loses his memory soon after during the Three Mile Island incident & Xavier rescues Scott Summers, Ororo Munroe & Pietro Maximoff from Stryker's custody.
-1986, Xavier and Magneto recruit Jean Grey.
-1996, Warren Worthington's mutation manifests.
-2003, events of
X-Men (2000).
-2004, events of
X2: X-Men United (2003).
-2006, events of
X-Men: The Last Stand (2006).
-2007, events of
The Wolverine (2013).
-2009, Wolverine is recruited by Xavier and Magneto to aid them in the Sentinel threat.
-2016, future sequences of
Days of Future Past (2014).
Timeline B (the bold represents the changes)
-4000 B.C., a teenage En Sabah Nur builds the pyramids.
-3980 B.C., En Sabah Nur, now an adult, bonds with the Apocalypse entity but is buried underground in a comatose state.
-1829, Victor Logan is born in Canada.
-1832, James Howlett/Logan is born in Canada.
-1845, Victor and James flee Canada to America.
-1861, The Logan Bros. fight in the American Civil War
-1918, The Logan Bros. fight in WWI
-1931, Erik Lehnsherr is born.
-1933, Charles Xavier is born.
-1933, Raven Darkholme is born.
-1944, The Logan Bros. fight in WWII; Erik Lehnsherr is placed in a Nazi concentration camp where he meets Sebastian Shaw; Charles Xavier's family adopts Raven Darkholme.
-1945, Wolverine is captured by the Japanese. Survives bombing of Nagasaki.
-1962, events of
X-Men: First Class.
-1963, Magneto is arrested for the assassination of JFK.
-1965, Wolverine and Sabretooth fight in the Vietnam War.
-1973, the events of Days of Future Past (2014).
-1983, the events of X-Men: Apocalypse (2016).
-2016, the events of Deadpool (2016); the ending of Days of Future Past.
-2017, the events of Legion (2017).
-2024, the events of Logan (2017).
So basically, in Timeline B, Wolverine never goes back to Vietnam but still meets Stryker - who
forces the adamantium bonding process on him. The man was
destined to become Weapon X.
And yeah, if you ignore Moira, Trask, Angel & Psylocke's roles in X3, the continuity isn't that big of a problem.