In Mega Man Maker, there are quite a few ideas that have not been fully realized or assets that were made inaccessible following further updates, but can still be uncovered hiding within the files of the game. Much of this content can still be accessed in-game with a little bit of elbow grease but is not available through normal means.
Caricarry from Mega Man 9 was present since the initial release of Mega Man Maker, though couldn't have been selected for use before 1.5.0, without editing the favorites/recent tabs, and was fully functional even then.
Gemini Man, coming from Mega Man 3, was originally going to be available from the launch of Mega Man Maker, with his data ported from the Make a Good Mega Man Level 2 engine. However, implementing him proved to be too challenging for several technical reasons, and thus was scrapped.
Attempting to play a level with the unused Gemini Man boss placed, will usually cause the client to crash upon attempting to spawn Gemini Man. By using text editing to place more than one boss, and spawning another boss before spawning Gemini Man, it is possible to load Gemini Man without the client crashing, but as the boss has no data assigned to it, it spawns as a 1x1 invisible solid tile.
Unused Level Objects
When a level object has been reimagined or relocated, the old version is kept for compatibility with older versions, but can no longer be accessed through the Level Builder.
Prior to 1.4.0, Checkpoints could only be used once when playing one stage, unless the player lost or restarted the level. However, the 1.4.0 version of the object deactivates previously gathered Checkpoints and the current status can be saved again if the player character moves from one checkpoint to another.
Until 1.4.2, Water was in the "General" category of level objects.
For 1.5.0, water was reorganized to allow variants, so a new category of tiles was created for the different water types.
Teleporters before 1.5.0 were listed in General, since Mega Man 9 was not implemented in the game at the moment. The only color available was pink, and they could be used to transport to a disconnected screen even if there was a boss.
In the 1.5.0 version, the Teleporter was overhauled to allow color variants and to be unusable if the teleporter sends to a disconnected screen and there are one or more bosses on screen.
Since 1.5.0 included multiple bosses, the Boss Doors had to be changed. The new boss doors cannot be crossed if there are one or more bosses on screen, even if they are touched on the side they normally allow to move. The old version was kept for compatibility.
In the music for the NES games, most of the music is included in all of the tracks. The Mega Man 1 tracks (excluding the Mega Man Powered Up ones) have the select screen, while the Mega Man 2 tracks have the title screen theme.
While not technically an enemy in this game, the custom cursor Pointkun has secrets of its own. These secrets come in the form of these 14(!) unused frames of animation that could've been used for multiple scenarios, including idle animations or editing text boxes.
It is, however, worth noting that the developers never intended to put these in the game. They were sprited without communication with the programmers, and the implementation of these animations was never attempted.
Wily 2 BG Alt
This version of the Wily 2 Background can be selected via changing the values of your favorites/recent tabs, just like the enemies described above. It uses shades of purple that more closely resemble the source game, but it is unknown why it was not implemented on the game.
Japanese "Rockman Maker" Easter Egg Logo
Though this easter egg was removed when the logo changed from Mega Maker to Mega Man Maker, the sprite is still in the files of the game. This easter egg logo was used from version 1.0.0 to version 1.0.9, and has been unused ever since version 1.1.0.
"Beefy Arm" Mega Man
Among the player, graphics are what appears to be Mega Man throwing something with a rather beefy (and miscolored) arm. This was originally meant for the Block Dropper weapon but was eventually replaced by a more accurate set of sprites.