The biggest problem is the titular villain. Apocalypse should have been THE villain. Instead, he was so damn forgettable. Putting aside the fact that he looked silly (the final product was no better than the original Ivan Ooze-esque picture), the performance was so damn subdued. There was no aura of power or presence. His scheme was absolutely nonsensical, the type of thing you'd expect to see from Cobra Commander. And despite all of his grand (and inconsistent) powers, the stakes never feel real. A forgettable character from First Class dies through an accident that [blackout]Havok himself[/blackout] causes. I mean, the whole destruction of the Xavier Institute is the result of Havok accidentally blowing up a generator. That is seemingly the extent of Apocalypse's threat level, the ability to cause an accident that [blackout]kills a minor character.[/blackout] Yes, there is the nuclear missile thing, but the movie forgets about it almost immediately. It is never given due weight and therefore is easily overlooked. Everything about Apocalypse is underwhelming. That alone is a death sentence to the movie. Apocalypse needed to carry this and he didn't.
The movie may have been better served by having fewer characters. It is hard to establish a villain when there are a buttload of characters who are shoehorned in. Was there any reason to make Storm, Angel, and Psylocke Horsemen? Considering how little time was spent on them it could've literally been any generic henchman. What a waste of Olivia Munn. But they are not the only unnecessary characters/moments. Nightcrawler is just there. He is amusing but doesn't contribute enough to the plot to justify his presence. Same is true of Jubilee (luckily, not much time was devoted to her).
The most egregious examples of unnecessary weight on the film come in the form of Quicksilver and the Weapon X subplot.
As to Quicksilver, his only reason for being in the movie is that he had a cool scene in DOFP. So he is shoehorned into this one, with a near identical sequence that goes on way too long and destroys the humor and charm of the scene in DOFP with complete overkill. Singer clearly has a hard-on for the character, but his role in the film just isn't justified, especially the weight that it is given. He is not just some bit player. He's the ****in' guy. He is the only X-Man to hold his own against Apocalypse (prior to Phoenix). He doesn't just hold his own. He beats Apocalypse down like a redheaded stepchild (which really takes away from Apocalypse and diminishes any effectiveness he had left). Now the obvious response to this is that his role in the movie is justified due to his connection with Magneto. That would be true if that subplot went anywhere. It is repeatedly eluded to, then when it comes time for the payoff...NOTHING HAPPENS.

It makes the whole character's presence and journey to that point feel like a waste of screen time and leaves the audience feeling cheated.
Further, the entire second act is pretty pointless. For example, the Weapon X scenes and Wolverine's cameo did absolutely nothing to move the plot forward. That entire half hour could've been cut without affecting the movie at all. The only thing of consequence that happens in that sequence is Xavier contacting Jean. That could've been done just as easily if she were sitting in her bedroom. The Weapon X scenes added nothing and took up time that could have been devoted to Apocalypse, the Horsemen, anyone else. It was such a weird part of the movie. It served no narrative purpose, was shoehorned in with no tie-in to the rest of the plot, and never came back up for the rest of the movie. Its not entirely unlike Stryker's extended cameo in DOFP. Singer seems to have this weird fixation on movie-verse Stryker. He seems to be operating under the assumption that he has created this timeless villain, on par with Magneto, who needs to be included in every X-film when, in reality, he is a pretty dull, cliche, military bad guy (Reverend Stryker of the comics was infinitely more interesting).
The Weapon X sequence kinda sums up the movie as a whole. It is disjointed and lacks an internal logic. A lot of random things happen, that are loosely strung together, then it ends. Oddly enough, the characters do not respond to things they ought to be responding to. [blackout]Does anyone acknowledge Jean turning into a giant ****ing fire bird that made her capable of eviscerating a god-like mutant? Storm changes sides because Apocalypse is cold about the death of some guy she barely knew. Why'd she do it? Who knows, we don't get to know her well enough to know the logic behind her actions. Hell, Scott barely acknowledges his brother's death![/blackout] None of these character moments happen, but we get a 20-30 minute Weapon X scene with no tie to the overall plot?
Don't even get me started on Magneto's arc. He loses his wife and child but never really has any emotional closure in that regard. He just kinda forgets about them half way through the movie and his plot becomes more about mending his relationship with Mystique and Charles than coming to terms with his loss. It makes the most powerful scene of the movie (the death of his family) feel hollow. Beyond that, when it comes time for his redemption, what ultimately causes it? Was it his ex-lover talking him down? Kinda but not really. Was it his son telling him that he needed him? Nope. That subplot is never even acknowledged. Instead it is some weird Tumblr-esque slash fanfiction montage of Charles and Eric's greatest hits.
In the end, it just wasn't very satisfying. The movie was all over the place thematically, was overloaded with unnecessary and underdeveloped characters, the villain was not effective and the narrative was not very compelling. What should've been the X-Men franchise's Avengers was instead a mediocre, soulless film. I think a big part of it is that the movie feels ashamed to be a comic book movie. I mean, Singer has never hidden his disdain for comics but at times it almost feels like he is apologizing for it. For example: "WAIT A MINUTE! THESE AREN'T SUPERHERO COSTUMES! THEY'RE FLIGHT SUITS! WE HAVE TO STOP EVERYTHING AND POINT THAT OUT! TEH REALISMZ!!!!" It causes the movie to shy away from the more fantastical elements. This showed in DOFP with the total under use of the Sentinels and now shows again. Apocalypse could've been so much more if Singer embraced it and just went balls to the wall with an uber-powerful demi-god. Instead, we have someone with all of the charisma of a feeble old man, spouting off pseudo-philosophical bull ****.
The best way to describe this movie is underwhelming. Even the action. While there are some cool scenes, the whole movie builds up to a final fight sequence that is little more than metal spinning around in the air, senseless destruction, and some quick shots of fights. Its not exactly Avengers-calibre action.
I really hope this is Bryan Singer's last foray into the comic book realm. It is telling that the best X-Men movie to date is First Class, a movie he had absolutely zilch to do with. This franchise needs some fresh blood. 4/10.
Oh, some other random nitpicks:
1) Why is it no one ages? First Class was set 21 years before Apocalypse yet Charles, Magneto, Moira, Beast, and Stryker all look exactly the same. I'm not saying to recast, but damn...age them up a bit with makeup. People change quite a bit in 21 years.
2) This film is very odd in the way it glosses over Charles wiping Moira's memory. First Class seemed to indicate that he took away her memory of the location of the mansion, nothing else. This movie retconned it so he wiped his existence from her memory. Xavier seriously violated Moira. That would be fine and consistent with the character, I have no problem with that. I do take issue with how it was handled. A mind rape is essentially treated as a joke throughout the movie. Then, when he does restore her memory, Moira's response is essentially "You gave me back the memories you stole from me when you toyed with my mind!? How romantic!"
3) I know I already said it, but damn Olivia Munn was wasted.
4) Did we really need an origin story of Xavier's baldness? It was kinda funny when Rogue's white stripe was given an explanation in the original X-Men, but did we really need an unnatural explanation for a middle aged man, probably in his mid to late 40s by this point, going bald?
5) Sophie Turner's American accent isn't atrocious, but it isn't very good either....also, the scene with her and Logan was creepy as hell. She (the character, anyway) is a 16 or 17 year old girl and she and Logan (a character who is physically about 45 years old and has lived for nearly two centuries at this point) have this scene where they look into one's another's eyes with all kinds of romantic subtext. Its creepy.