Let me start out by saying the legitimacy of this being a prototype can’t actually be confirmed. Nintendo has not been responding to emails about it, but there is a lot to like about what this provides. The fact Nintendo also wont open up about it is a sign it most likely is the real deal. Material like this should of never gotten out of the home base, but thanks to a fan at Lost Levels we can now see what some of the original design for the game was before the finished product.
For starters, the game was easier in it’s earlier days than in the final version. As you can see on the left (which is the prototype version) they had easier types of enemies than in the final version (shown on the right). A lot of health pools and spawn rates from the prototype version were also increased in the final version, making things that are already difficult to kill even harder.
In addition to those changes, several of the dungeons had different types of maps. Some of them got flip flopped with other dungeons, while others had rooms completely removed. The music is different (apparently the theme is simpler) and the maps we’re different.
While I wont link to direct downloads of disc copies due to the nature that, if this is real, is most likely illegal to distribute, what I can link you too is a page on The Cutting Room Floor. This page documents all the significant changes between the versions, including several bugs and things about the game that simply were not complete at the time, such as all the sound effects. This is indeed a rare discovery, and really, I wish publishers would just openly release this stuff say, 5 years after a game is made. It’s just really neat to have an inside look at the earlier stages of a games creation.