Maximum Ride/WMG

The "apocalypse" that Maximum Ride is supposed to save the world from is Angel
She can control and read minds, developing new abilities at an alarming rate, and it has already been commented that she is liable to decide that she wants to conquer the world.
 * Going along with this, Angel is only faking being good. Remember in the third book how she joined the bad guys for awhile? That was legit. She only made Max think she was spying for them because they decided that Angel would serve a better purpose with the flock. Also, she faked getting stuck in the crevice in the fourth book. You're really telling me that someone with all those powers would get stuck that easily? No dice. She totally faked it knowing that she'd be rescued, making them sitting ducks for the bad guys to capture them.
 * Another point that goes along with this idea, which I happen to like a lot: Angel's a Deconstruction of a Mary Sue. She gets all those epic powers and is adorable, but it's been established in book 1 that her moral compass is awry at best. She's a little kid too, and the "baby", but and even Max is disturbed by her. Her judgement isn't always for the best, either, but being able to make decisions ala Chessmaster obviously appeals to her. So what happens when a Mary Sue with her perfection gone to her head and lacking in a conscience tries to team up with the Mad Scientist?

The Flock didn't really have bird DNA inserted into theirs.
Ignoring the utter implausibility of Lego Genetics, if you've had avian genes inserted into your DNA, you've just had avian genes inserted into your DNA, you don't start spontaneously acquiring powers. Really, The School mutated their DNA to resemble that of a bird's, and lately they'd been mutating randomly. The truth is that Maxumum Ride takes place in a Marvel-like universe, where mutation = superpowers.

Tokyo Mew Mew is a result of School scientist Ryou taking the Flock's words to heart and making a Heel Face Turn.
He perfected genetic engineering becuase Evil Is Dumb and decided to assign Petting Zoo People to save the Earth.

The bad guys throughout the series are actually working for Abstergo.
The flock was actually created in a Templar experiment. Angel is especially important because in addition to being a human/avian hybrid she also has genes from "Those Who Came Before!" On top of this, her continually developing mind reading/control abilities mark her as the result of a Templar attempt to create a living Piece of Eden. Max is important because she has Assassin genes in her, making her immune to Angel's mind control abilities. The other members of the flock are simply offshoots of this research and are considered superfluous by the Templars.
 * The story is thus...having been thwarted on multiple occasions in their attempts to establish a mind controlling dictatorship over the rest of humanity (by the Assassins, of course), the Templars have opted to take their plans to the extreme and have instead decided to bring about the apocalypse, wiping out their enemies and most of the useless humans in the process. In the new world created by the Templars, only their chosen superhuman subjects will be allowed to exist, being ruled over by the Templars, who are hoping to evolve themselves into beings like Angel. Max was created as a sort of counter, in case Angel ever went rogue or was used against them.

The explanation behind the Canon Dis Continuity of Max's hair color
Max started off the series with dirty blonde hair which she just called "blonde" it probably got a shade or two darker since last mentioned, so she just called it brown.

All the thrown away characters...
...like Anne, Marion, Sam, Lissa, and the like? They're all working for the school(Well, we already knew this for some of them)

All of the gaping plotholes, random events and unrealistic coincidences were actually planned out.
James Patterson is a famous thriller writer, and thrillers are mostly plot and tension. While to the readers it may seem as though he's just making the story up as he goes along, he actually has a master plan in mind, one that will be both complicated and simple at the same time, tying up all the loose threads and causing us readers to scratch our heads and wonder why we didn't think of that.

Dylan is...
...a clone of Gazzy. He was created to destroy Angel, who shall someday become an Eldritch Abomination.

It's not real.
The last chapter of the last book will be something mind bendingly awesome only to cut off right before it ends. Max and her friends will be revealed as normal teenagers in a simulation game. Alternatively, she was just telling her little sister a bedtime story and got carried away.
 * If it was just Max telling a bedtime story and getting carried away, it would certainly explain why the story feels like it's being made up as it went along.

It's a book inside a book.
Similar to the above WMG, the fourth wall breaking isn't just to make it more interesting, an amateur writer is actually writing the books. The last chapter will have him/her try to get it published, only to be turned down/critisized because of the exact problems people have with the books in real life.