I tackled some of the plot holes in the link that was posted earlier
The 20 Biggest Mistakes in the X-Men Movies - CraveOnline
1. Professor X's Body: Not a plot hole that is Patrick Stewart on the bed on the X-3 after credit scene. The commentary on the DVD confirms it is him and that it is Xavier’s twin. Also, it seems that his powers are somehow connected to his paralysis in DOFP so that might explain him in a wheelchair. What makes no sense is how he is walking and using his powers in the flashback in X-3 and X-O though, unless Beast perfected the formula.
2. Cyclops's Age: Cyclops is in high school in X-O, which means he is in the age range of 14-18. X-1 is set in 2005 according to the timeline and X-O ends in 1979. That would make his age 40-44. That is still kind of bad, but he isn’t 50.
3. Wolverine Remembers World War II: He also remembers Kayla because we hear him calling her name in his mind in The Wolverine when he wakes up in the chair. We see in DOFP, when Xavier looks in mind that he remembers Victor breaking his bone claws in X-O fight. So, he remembers more than just WW2, he could be regaining some of his memories, but it is hit and miss because he does not remember what he was doing in 1973.
4. Magneto's Helmet is Half a Century Old: Good point, Xavier should be able to remember the helmet. Also, another strange thing is that the helmet changes the movies, so it might be that Magneto makes new ones to keep up with Xavier’s growing powers. So it could be that when Xavier was connected to Cerebro his telepathy was strong enough and had the range to detect Magneto until he updated his helmet to the X-1 design.
5. Moira MacTaggert's Age: It is a hole, unless the movie version created a way to give humans powers like in the ultimate universe, but there is nothing to support this in the films.
6. There Are Two Emma Frosts: The issue isn’t that there are “two”, it is that Emma Frost (January Jones) dies between First Class and DOFP, so the Emma Frost in X-O can’t be the same character because the end of X-O is set in 1979. Emma (X-O version) and Kayla could be Emma Frost’s (First Class version) daughters. It would make sense since Kayla has telepathy and Emma (X-O) has the diamond skin.
7. Wolverine's Adamantium Claws Grow Back: Magneto would probably give him his metal claws back because he would need them to fight Sentinels; we see in the 70’s portion of DOFP, Wolverine can fight Sentinels with the bone claws, but it is hard for him. Also in X-2 Magneto remarks that he is one of 2 people that can manipulate adamantium
8. Wolverine's X-Rays: In the comics, Wolverine’s healing factor made a molecular change in the adamantium that resulted in admantium beta which functions like true adamantium, but does not inhibit the bone’s normal processes, so supposedly it heals as well if it was ever damaged (Which isn’t an issue since it seems more durable then the film version metal) which doesn’t make sense at all really. Wolverine even regrows his entire body with adamantium and all at one point (I’m not talking about the Marvel Civil War where he is reduced to a skeleton). It could be that the film version has adamantium beta as well, but it takes longer from the adamantium to “heal”. The whole metal “healing” is silly though, since his body treated it as a foreign substance and without his healing factor he has to take special drugs to combat the metal poisoning.
9. Magneto Didn't Help Build Cerebro: This is a big one. Since it has been revealed that Magneto has been imprisoned under the Pentagon for the JFK assassination which happened on November 22, 1963, and First Class ends in 1962. So, there is less than a year that Magneto could have helped Xavier build his Cerebro in the mansion, but Magneto helping Xavier build seems unlikely with the dialogue in DOFP.
10. Wolverine's Amnesia Timeline: Unless Xavier is just awful at reading Wolverine’s mind through his adamantium skull, this is an issue.
11. There Are Two Bolivar Trasks: This is like the Emma Frost thing, in the ORIGINAL timeline Mystique kills Trask, so I am not sure who that is in X-3. It can be viewed as a plot hole though.
12. Beast Invented the Mutant Cure: Beast did not invent a “cure”, it merely temporally suppressed powers if taken in large doses. This is explicitly said by Beast to Logan about Xavier using too much to suppress his powers. We also see Beast use a lot of it to fool the Sentinel into thinking he was human. In X-3 Beast is no longer hiding his blue form and could simply be surprised that someone find a way to completely suppress mutant powers, however we know now that the cure was not permanent.
13. There Are Two Sabretooths: Victor could have either mutated further naturally or due to Magneto or William Stryker. Magneto has a machine to turn humans into mutants, I’m sure he could have made one to increase mutant powers. The further mutation could have affected his memories. Also, Toad appears to be more mutated in X-1 than he was in DOFP.
14. Professor X’s age: This is a plot hole, the only way I can explain it is that Beast perfected his serum since Xavier is walking AND using his powers, but maybe a side effect could have been Xavier aged rapidly to a certain point kind of like how Beast become blue in First Class.
15. Wolverine Is Not Unique: Yes he is, he has the only one naturally to be able to survive the adamantium bonding process until Lady Deathstike that is which Strkyer points out in X-2. We see in Origins that Sabertooth, according to Styker, could not survive the process (which could have been the motivation to side Magneto if he could enhance his powers). In X-O, Stkyer also need Wolverine’s DNA for Deadpool.
16. When Professor X Met Magneto: This one was covered well in the link.
17. Kitty Pryde's New Powers: All I’m going to say is I wish this was explained, it could have been so simple to say she developed it has a side effect of her original powers.
18. Mystique's Age: Personally, I hate the plot point of a character losing their anti-aging power and then their age catches up with them. That basically means the whole time they are not actually healing age related damage but covering it up. They did it in The Wolverine and X-1 with Wolverine and it annoyed me because it doesn’t make sense.
19. Mystique's Powers: I think her shifting abilities only allow the Sentinels to use other powers that have been pooled from mutants. We see one that absorbs Colossus’s metal skin (Rogue), one with diamond skin (Emma Frost), and one using clawed fingers (could be Sabertooth or Lady Deathstrike).
20. Wolverine's Mind Doesn't Heal: Yes it does, in the comics Wolverine’s amnesia is partially due to his mind covering up tragic events to keep him mentally stable. As, I covered earlier he has regained some of this memory in the films which really isn’t a representation to his mind “healing”, but still.
I'm going to enjoy the movie regardless of point holes just as I enjoy The Avengers movies despite their mistakes, but some "plot holes" are just things that are not fully touched on in the films and I'm fine with that I don't need every plot point spoon fed to me.
Also, since Marvel gets money from the X-Men films reducing the popularity of the characters will only further hurt them, but as I stated earlier X-1, X-2, and X-O are the only ones to have toy lines anyway that I am aware of.