Hello!
You know something I'd like to see in "Brothership" but that would be heartbreaking?
Conflict
I mean, we know these two love each other so much, but they're still brothers. And if the whole theme of the game revolves around their brothership, then it should be put to the test at some point. At least in order to make the player believe that these two would fight and separate by their own choice. Not "separate" like when they arrive at the ship separately, but "separate" because they are fighting about something, and the villain manipulated the situation to keep it that way because he knows that it is their brothership that would ruin his plans.
The issue with that is I can't really think of a situation where they would believably go their separate ways. Not in the Mario & Luigi RPG canon. They've already gone through like... five major adventures where they were the ultimate, inseparable team through thick and thin. To get them to willingly split over a fight, even one orchestrated by outside forces, would take a wild set of misunderstandings.
However... a meataphysical threat that divides them? A villain directly altering the mind of one of the brothers in order to ruin their bond because he knows what an effective threat they are as a team?
That I can get behind. Mario is long overdue for a brainwashing anyways.