The whole "Building the world" similar to Legend of Mana is actually a bit of Gameplay and Story Integration if you think about it - since technically, Marche and his friends created the world using the grimoire, that's actually Marche imagining where things would be. (Although some like the palace and Ambervale are in pre-determined locations)
Because Marche didn't place them; Mewt did.
Some people laugh at Marche, Ritz, and Mewt for having such silly wishes...but consider that they're at least twelve years old. Twelve-year-old kids are of course going to do stuff like wish for their hair to be naturally red so bullies won't bother them, for their dead mothers to be back in the family again, and for their bullies to meet cold deaths in the snow. Of course they won't think of the consequences of their actions - they're little kids.
Likewise, Doned's actions are going to make a bit of sense when you consider he wanted to walk and run like other kids...and if you interpret Marche as a Villain Protagonist, he thinks Marche is going to destroy it all for him.
Why out of all the kids is Marche the only one who tries to escape Ivalice? Ritz gets her natural red hair, Mewt gets his mother back and his deadbeat father turned around, and of course Doned gets to be healthy. Think about it, what does Marche want? What does he get? That's right, Marche is the only one of the group who doesn't want anything, he gains absolutely NOTHING and loses just about EVERYTHING from being stuck in Ivalice. He has a simple, largely stress free life, then loses that life and goes to a world where he has to fight just to survive day in and day out. For Marche, Ivalice isn't a dream come true, it's pretty much his own personal hell.
See third Fridge Horror below, With things like Child Soldier, monsters that would give nightmares to Real Life hardened soldiers, matched fights just to survive another day, permanent death for sentient people if Ko'ed in Jagd, and possible PTSD you would also simphatize with Marche.
If you check out all of the character's stats during the tutorial snowball fight, you can see Mewt is the only kid who has a point in Magic Power while all the other children don't have any. This is a reflection of Mewt being the class librarian and how he reads lot of books, which is usually associated with wizards and mages in traditional fantasy settings. Guess what Mewt becomes when he's transported to the fantasy Ivalice?note Although Mewt doesn't actually fight in the game, it is implied he does have some sort of power since the world was shaped from his wishes and desires.
In an early mission, you save a professor from three 'lost ones,' the animated corpses of people that are lost in the snow. Their names? Colin, Lyle, and Guinness, the three bullies from St. Ivalice. You then proceed to kill/exorcise them. Later on, you fight them again, this time as vampires.note You do see the three bullies at the end of the game, so they were apparently restored when the rest of Ivalice faded away. But there's more fridge horror. Do they remember?
Even worse is the fact that everyone in Ivalice is someone from the real world with another personalty forced onto them and the kids are rather okay with it.
What about the fans who are OK with it and insist that Marche is evil for restoring things to the way they were?
Marche had no idea exactly how things worked. He knew some people got carried over but not that everyone else did too. Babus even tells him he has memories and experiences of his whole life. Replaced people or not they're still full people with full histories. Yes he wants to restore the old world, but it's not until the last moments he does so in any way other than completely destroying the current, existing, and very real one.
There's a mission where you have to investigate mysterious stabbings who turns out to be a tonberry. Does that mean that in the real world, there is a serial killer on the loose?...
The scene where the real world transforms into Ivalice includes random bystanders turning into monsters. That's right, the main characters might be better off in this wonderful fantasy world, but there are plenty of other people who now exist to be beaten up over and over until they either die in a Jagd or are captured and sold into slavery. It might actually help justify Marche's actions.
Also, the "Fire! Fire!" mission, involving the player having to stop a group of Bombs from burning down a neighborhood, with the implication that if you fail, the judge watching over the fight won't do a damn thing to stop the arsonists.