As for the stamina bar, that can be disabled in the settings. Just open the script editor, go down to the section called Settings, and find a constant with STAMINA_BAR in the name and make it false. It's currently coded to show the stamina bar by default, and tiredness animations if the stamina bar is disabled. However, there are no animations for that yet, so you won't have any indication of your remaining stamina.
The item system has already been partially re-written to be more like FoMT, so you won't hold tools over your head in the next release. It was initially designed to be like HM:MM, however it would require a lot of spriting to show the various tools in the player's hands in a visually appropriate way. Therefore, it will be downgraded to the FoMT style.
@Varion: those screenshots are only a tiny indication of what's in this project. The mountain where you can pick up items to ship in the shipping bin (and the shipping dude who comes and picks them up), the mine where you can dig for coins and stairs as well as break rocks for ores and gems, and the farming system which allows you to grow crops just like in the actual games weren't included in the screenshots just yet, so there's a lot more to love in the project itself.