Ok, here I go.
I'll begin with the most obvious one. Why do they send Wolverine back in time to the 70's in the most chaotic time possible? Xavier is a junkie, Magneto is in prison (not to mention he's Xavier's "enemy"), and Mystique is on her own god knows where and she's now "crazy" or something. They are in the future and can choose pretty much any time to send him back, so why not a few years back when they were all still together and on good terms? If Kitty can use her new powers (that's another one) to send wolverine so far back in time, why can't she send him to a more peaceful time, which would make it easier on them both. Just a few years earlier would have been less complicated.
Why not go back in time to simply ask Xavier to mind-rape Bolivar Trask into liking mutants and destroying his sentinels in secret instead of just stopping Mystique from killing him? Doesn’t look like a full long-term solution. If Wolverine could convince Xavier to stop using his drugs, they wouldn’t even need Quicksilver to free Magneto from the Pentagon.
Also, Wolverine is sent back to the 70's to form a team with Xavier and Magneto to stop Mystique from killing Trask? Why is that again? Both Magneto and Xavier are completely pointless in the original task of stopping her at the Peace treaty meeting in Paris. Wolverine could just have waited for her in Paris and the outcome would have been the same. He already knew where she was going to be. Magneto and Xavier were not needed, if anything they complicated things.
Then there's the pentagon sequence. Why was Charles Xavier there? He had no powers and doesn't contribute in any way since he's just some skinny normal guy. Quicksilver frees Magneto, Hank disrupts the cameras, and Wolverine is the tough guy in case of a fight or something, so why did Xavier show-up? No reason for him to be there.
Then, there's the time lord, Quicksilver, he experiences time faster than everyone else , which is why he can play around with the guards while the bullets take almost a minute to reach their targets. The whole conflict of the movie would have been resolved if Wolverine or Xavier simply brought him with them after he helped freed Magneto. Their plan was to catch Mystique... but if only they had a time-God with them that could catch Mystique in less than a second and take her out of the building without anyone noticing. In fact, why even rescue Magneto to begin with? Wolverine has a secret weapon, the boy in grey
Also, while Quicksilver is running he's listening to "time in a bottle’" on his 1970's Walkman while he beats the guards in the Pentagon kitchen even though the whole sequence lasts 0.005 second in real-time. Quicksilver might be godly fast, but his 1970s Walkman, not so much.
Before or after the pentagon scene we see Mystique rescue some mutants. Well, that's nice of her, but her plan sucks, since Mystique didn't incapacitate or kill William Stryker who left the tent and identified the plane that the mutants took to escape. He has legal authority and could just reorder the plane to land and they would be *****. So Mystique’s introduction was pointless .
Also, if Mystique can change her body mass to adapt to any form like a T 1000 , why doesn't she always fight as a 7-foot-tall bodybuilder UFC fighter filled with steroids every time she's in a fight?
Then in Paris...or wherever that was, Trask uses his Ghostbuster mutant detector to find Mystique hiding as a Vietnamese general and then he ORDERS the soldiers to arrest her. Nice going! One problem, Trask has no authority...ZERO, he is not the government, he is not on American soil and more importantly, he is not even dealing with American citizens.
Is it common for midget tourists randomly asking for someone’s arrest based on their Toys-R-Us gadgets that no one has seen before? Yeah, Mystique’s cover would eventually get blown, but it’s stupid to see the guards and the Vietnamese generals completely agree with Trask the second his plastic toy tells them one of their comrade is a mutant ...something by the way, most of them never heard of before. Mutant? What's that? Is this little foreign American guy calling us mutants?
Eventually, Xavier decides to become useful and a productive member of the team, instead of a sad junkie, so he regains his psychic abilities and he finds Mystique at an airport and at first tries reasoning with her, but when that fails he uses his not so secret weapon, mind rape....yeah! That **** never fails! Oh, but he says he can’t do it because Mystique doesn’t want to. Really? If mind rape is only possible when your victim wants it, it wouldn't be a very good mutant power. In this film franchisee , EVERYONE is defenseless against Xavier’s mind control, except for Magneto because he uses a ******* specially designed helmet. The only way someone could stop the mind rape, is if he or she also has those psychic powers, like Jean...that's it. Maybe a jedi, but even they wouldn't stand a chance against Xavier.
Later on, Magneto develops new powers
Not only can he manipulate metal, he can also separate it to the microscopic level and implement it to giant robots he never saw, in the dark, in 8 different train cars at the same time, in order to hijack their electrical components he never saw, which puts him very close to omniscience. Hard to believe he got shot in the neck the next day
And why didn’t Magneto simply use his robots to kill everyone at the White House in front of the world to establish that using robots is not a good idea, completely shut-down the Mutant fear and never exposing himself? He could just be seating there in the crowd wearing a cool hat, controlling the robots. Flying with a baseball stadium looks awesome , but a lot less logical and a lot more dangerous for him....he could get shot in the neck by a METAL bullet
On a side note, why didn't the government buy Trask's 15 foot plastic robots? Even if they didn't care about the mutants, they are still in the middle of the cold war. I'm sure they could find some use for them. They are giant PLASTIC robots in the 1970's!!! It would be a miracle of engineering to make such a thing today out of metal
There's no way the US government wouldn't be interested in them.
Then the final scene of the movie where Wolverine wakes-up to find all his buddies alive and teaching at the school. Great moment, but it doesn't make sense for Wolverine to wake-up in the future and not remember anything since he last drowned at the end of the movie. Here's why, his future consciousness was sent in his younger self to change the past and he succeeded.
This means the Terminator future never happened and we get to see the nice future where everyone is alive and well. But young Wolverine who was "taken over’’ by Older Wolverine would have awaken from his incident in the 1970s without remembering anything from his past week, BUT from then on, he would continue his life and the older Wolverine simply stopped to exist. It makes no sense for younger Wolverine to get a little older, become a teacher at Xavier’s school, and one day, have his consciousness destroyed and replaced by Older Wolverine’s consciousness that was dormant somewhere. Older Wolverine stopped to exist the moment the past changed.
I didn't include any inconsistencies that involve the older films, because that wouldn't be fair to this film and there are too many anyway.