In Mega Man Maker, there is quite a few of ideas that haven't been fully realized, 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.
This article is a work in progress. If you know anything about material that exists within the game that isn't accessible, feel free to add them at your own leisure
Caricarry from Mega Man 9 is in the game, though cannot be selected without editing the favorites/recent tabs, and is fully functional; Shooting it will slowly causes the rocks it carries to get dislodged and potentially damage you.
Both variants of the Petit Devils, also from Mega Man 9, can be selected via editing the favorites/recent tabs, and both versions work as you think they would, splitting into smaller devils upon getting hit too many times.
While not technically an enemy in this game, the custom cursor Pointkun has secrets of it's 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.
There are a lot of unused music tracks in this game, nearly all of them being slower, chiller versions of existing Mega Man tracks, similar to the music used in the Tutorial.