The main differences between the Wii edition and the original are the vastly upgraded graphics and the new third-person camera angle, first used in Zero: Tsukihami no Kamen. The map has been updated to work better with the new viewpoint, and the costumes were designed with more emphasis on the back since it is constantly in the player's view.
Also similarly to Tsukihami no Kamen, the game contains "ghost hands" which may randomly pop up when the player attempts to pick up an item. If a hand appears the player will have to pull back Mio's arm or will have to shake it off and incur damage.
The game now has a brand new peeping mechanic which allows you to see many new locations and things that weren't in the original game, as well as many newly created objects that can be opened, moved, and ghosts also have many new attacks and special abilities for each one of them including Dark Return's which is an updated version of Blooming from the 4th game which grants them even more new attacks and abilities.
Several areas throughout the game are newly accessible, such as the shores of Whisper Bridge, the atrium of the Ōsaka House, a new hallway in the Kurosawa House, and the room on the top floor of the Kiryū House which could not be explored in the original.
Several of the outfits from the original game, including the Yae and Sae costumes, have been removed and replaced with new costumes.
The Camera Obscura, while its external aesthetics are identical to that of the original camera from the PlayStation 2 release, has a new viewfinder and re-worked controls, a Lock on function, a revamped upgrade system, a completely new way of using lenses, and newly created lenses.
A new mode, Haunted House, has been added, a mode in which players slowly walk around a set course in first person and scary events randomly occur, the player can search for haunted dolls while a one hit kill ghost chases after you, where you can take pictures of ghosts from the game and receive rankings on your spirit level (based on your fear meter that amasses when playing), a second player may attempt to scare you by pressing buttons on a second wii remote and causing random events to occur, and where the player may learn the backstory of new character Kureha. This new mode replaces Mission Mode and Survival Mode.
Each time you defeat a ghost several newly created lines of dialogue for said ghosts come out of the Wii remote
A two-player mode is now supported in the main story where a player with a second Wii remote can take Syncro shots and deal double damage to ghosts as well as hear newly created dialogue come out of the Wii remote.
The amount of healing items in the game has been decreased and some fights that were optional in the original are now mandatory.
A mini-map as well as the system that shows the player where each key goes from Tsukihami no Kamen has been incorporated into this game.
A few unexplained occurrences in the original game are now resolved such as what Mayu was doing in the doll room during chapter 3, and the identities of the two hanging twins in the Ōsaka House cutscene in chapter 1.
Over 15 new cutscenes have been added to the game that further expand upon Mio and Mayu's relationship as well as build upon the world of the game in one of the new endings.
Several of the cutscenes in the original have been extended to be more complete and have more information of the story and characters given in them.
The way the player obtains the endings in the game are no longer determined by what difficulty has been selected. Endings are instead determined by how you play the game.
The game receives two completely new endings in addition to the ones obtained from the original and Xbox versions.