This is of course nothing official, it's just my take. I'm a freelancer pixel artist aand.. let's begin (?)
GUI
So, first of all let's talk about the one following us around for the whole engine: the GUI. As Wuzzy suggested, we have 9-slice images, so why shouldn't we use them? We have one problem though: how can we design a GUI which doesn't resemble any specific game, but, on the contrary, an engine? These are my two suggestions:

The first one uses the cubes children usually play with (or at least, I guess so?), to learn how to make words, or just to make some tower and tickle their creativity. On Minetest people don't learn how to read, but for sure learn how to build any kind of stuff - code or actual buildings. The second one, which is actually the one I prefer, is made with cubes which are pretty basic: grass/dirt, water and stone. Less details, more focus on the top right corner with some vivid colours and that's it.
This could fit well both as the pause/volume/keys/whatever menu and on the main menu. Speaking of which...
Main menu
So, the first thing people see is the main menu. Which is, right now... not good. I thought about sticking to a simple design and I was inspired by this.
First step (the logo is just copy-pasted, don't mind its quality):

What we have here is me opting for a classic main menu even if we're talking about a hybrid (engine/game), because few straightforward elements won't confound the user. Now, the words I used may not be right, but I challenge anyone to not understand which does what. In other words, it's kind of a landing page.
Great, but now it's kind of empty. And here again, anonymity kicks in - sigh. What background could suit without unbalancing the narrative toward this game or that game? Probably no one, so how about choosing a theme for the engine? I thought about creating just a pattern as background (kind of like the forum), or simply doing an illustration with an ethereal vibe. This is just a sketch, so I'd like to know your thoughts before continuing; basically, I used a heavy aerial perspective to avoid detailing things and the consequential de-anonymisation, playing just with silhouettes

I want to specify I have sketches on paper about the other sections too, it's kind of well planned (or at least I hope so :D)
Let me know people :)