I dunno why I'm awake now instead of later, but I suddenly woke up and felt weird, so I started playing SM64 (this is like the beginning of a creepypasta, I know) but at least in this 'didn't really sleep enough' mindset, I can definitely see what people are talking about when they say this game is creepy - and I think it comes from viewing it through the lens of someone who's already seen what will come later in 3D games. Going this far back, it feels sort of... fake. These paintings and the castle itself don't feel like real places. Nobody lives here. Nobody dies here. Nothing exists in these paintings beyond the minimum of what you need to collect stars, and the ground abruptly drops off into a void past where it needs to be. Even OoT feels so much more real and lived-in. Even the little things that try to 'justify' the stars like the captain's note claiming that the star is their treasure in Jolly Roger Bay feel artificial, like it's just enough to make sense as long as you don't think about it for longer than a few seconds. ..And then you do, and you realize that not only did Bowser hide the stars there just recently so this 'captain' couldn't have had that as an old treasure, but the whole 'find my treasure if you open the chests in the right order' thing doesn't quite make sense - and wait, why is the bay completely surrounded by rock walls with no way out-
. . .Yeah, I can definitely see why this game is creepy. It's still a fun game, and it can be cheerful and lighthearted when it wants to, but there's something off about it.
Compare that to SMRPG, because really that's the Mushroom Kingdom we're leaving before we go into 64's version - there are actual towns, people have families and jobs and can be put in danger and saved from it. A couple joyfully tells you that they're going to be married soon... and then they actually get married. They even have a honeymoon. And this all largely takes place in the background while you're focusing on your own story, because that's how a real world works. Not forgetting that Raz and Raini first speak to Mario as if they're old friends who've known each other for a while. People from different towns occasionally reference each other. And then there's that chase scene on Booster Hill where you can look out into the distant background and see all of the other locations, exactly where they should be in relation to each other, and you understand that you're in a real, consistent world - this is here, and that is there. We don't even really get that again until Sunshine, to put that into perspective.
You get the impression that this is a real, living world that people inhabit and things actually happen there, constantly, whether you're looking or not. Now, I understand that there would obviously be some trouble translating that to early 64 titles while they were still figuring things out, but like I just pointed out OoT managed it well enough. These early titles are a mixed bag, honestly - some of them can be pretty okay in terms of feeling like actual places, but then some of them just feel wrong.