There is accounting for personal taste.
My best defense is that Brian Singer and the writers set a high bar for the first two movies including an atmosphere that was highly appealing to me. Xmen3 lost that, but it was acceptable. I thought Wolverine Origins revived that vibe and it focused mostly on one character instead of the ensemble. This is always preferable for myself, revealed by the fact that I love Thor 1, and like Ironman 1&2, but am not a big fan of The Avengers.
In the first 3 movies The Professor and Magneto were advisories but they had some level of respect for each other, as far as I know, in the comic, they were never friends, but I have not read every XMen ever published. Magneto was painted as a bad egg from the start with his belief that "Homo-Superior" (versus Homo-Sapien) is the next step in the evolutionary ladder and deserved to rule the world.
First Class was a weak ensemble story and I objected to the Professor and Magneto being buddies.
For The Wolverine, I remember the XMen (not just Wolverine) did venture to Japan to fight these IronMan type mechs, but don't remember anything about a WWII Japanese guy wanting Wolverines regeneration abilities. Maybe I have forgotten. I disliked most of the characters in this film and the Wolverine is starting to look old.