Stories marked as ‘FC’ will continue the established relationships and facts as presented in the movie X-Men: First Class, mostly affecting the ‘older generation’, including Mystique.
Everything set during and after the movie X-Men Origins: Wolverine, but before X1, will be marked as ‘W1’. This means Logan can meet Marie under different circumstances without using the AU ‘verse, as long as the facts and relationships presented in the first Wolverine movie are respected.
The story is set during or after the first X-Men movie. This can also be several years after X1, because when X1 is used, X2 and X3 never happened.
X2 means the story is set during or after the second X-Men movie. X3 never happened.
Yes, there is hope after the third movie. X3 stories are set during or after X3.
‘AU’ stands for ‘Alternate Universe’. Warrior!Logan and Maid!Marie? Or Repairman!Logan and Girl-Next-Door!Marie? Egg-Juggling-Clown!Logan and Mother-Of-Five!Marie? In AU it’s possible. Sick and tired of scarves and gloves and mutations, but not a fan of X3? AU is the right setting. You want a completely different turn on the movie with bits and pieces of X1 and/or X2 and/or comics? AU is your place to be. In other words: anything goes. God bless AU. Amen!