The original release of the game.
Released 2/27/2015, version 1.1 was released to fix various issues with the game to make it more "enjoyable". Changes that have been noted are as follows:
As ESS bottle duping is essential for speedruns, it is recommended to not update to the 1.1 version. MM3D does NOT require 1.1 to launch. If you do update, you can simply delete the patch data by going into your data management settings and deleting it.
A while after the release of 1.1, every print of the physical game now come with the patch preinstalled. Due to this, it can't be deleted and it is thus recommended to buy the digital eShop version instead.