Majora's "darkness" comes mostly from its story, we can hardly tell anything about BOTW2 yet but comparing the tone of this trailer to BOTW's reveal trailer makes it pretty obvious they're going for the "serious" lean of OoT/MM/TP rather than the "wondrous" WW/SS/BOTW.
Aesthetically it's probably going to fall between OoT's bad future and TP's "brown/grimdark." But that's assuming there's going to be a major overhaul/transformation of the overworld, since as it is it would be extremely hard to get any sense of an "oppressive" atmosphere from BOTW's wide-open fields that make up half of its map. And actual "darkness" comes from story/writing elements that we know nothing about, all we really have is a sense of the tone that's been set with creepy dissonant music playing over dark ruins and scare montages and a living corpse.
I read Aonuma's statement as comparing the tone against BOTW, not Majora. It's still obviously a major tone shift, like walking out of the Temple of Time and seeing the sky is red and the town is full of zombies. I wouldn't be concerned that they're not taking it seriously.