The A-Engine: A new Beat 'em Up game engine

[Som1Lse]

But these aesthetics would compensate, don't you think?

For what? A feature I could just as easily have had with the same aesthetic? Not likely.

Plus, I find it rather innovative to have as little UI as possible.

I'd find a spacecraft made out of marsbars innovative, but I'd still prefer a regular spacecraft if I ever were to use one. I find innovative in this sense to be no more than a buzzword.

There has been a lot of drama in the anime about the ship being the natural home of pirates, and a symbol of freedom in general. The author has provided the ship with great detail, to the extent that he drew "blue prints" for it, and it would be a loss to not have the ship in somehow in the game as well.

In that case I'd put it in the actual game rather than the main menu, if it is used in the main menu then great, if you can walk around it at the same time then great. But don't compromise something which works flawlessly already.

I myself really like the idea of having the game start with you controlling a player on board of the ship, allowing exploration of all the different rooms in it with animated NPCs and all.

I don't have much else to say except for: I don't. If the ship used for the main "menu" is small enough to fit on the screen without any scrolling, then there is no reason that I can see why you can't just click on the elements. If it is larger than the screen, then seriously consider why I would have to walk that large a distance to change the options and choose between modes.

It also allows for a great deal of easter eggs, minigames, and these small details people are fond of.

If you were to allow walking around the ship as part of the main menu while still having things to click on, then it wouldn't be an issue. If it is too large for this, then reconsider whether or not it is worth the time it takes to walk around the ship in the first place, if it was included as part of adventure mode, then the easter eggs could still be hidden in the ship.
Lastly, if you want to sacrifice functionality for the sake of a few easter eggs, then it's probably not worth it.