You might enjoy crpgaddict, a blog that is playing through every computer roleplaying game in chronological order, providing scores for each one on various metrics. The reason I bring him up is that he doesn’t rate on a curve, or give things marks for being “good for its time” - if pool of radiance scores higher than skyrim, it’s not because it was influential or good for its time, but because he thinks it’s outright better regardless of age (just an example - I’m not saying he would actually rate those two games that way, and he has not rated skyrim). There are early 80s games that he remembers fondly and had a huge impact on the industry that he rates as like 23/100 or whatever, because the scale leaves room for the Witcher 3.
It takes a long time to get through all those games, so he’s currently up to the early 90s, having updated his blog regularly for over a decade. But his list of highest rated games might be a good place to start.
Oh, and while we’re talking about old-ish RPGs that would score well on his scale, I might as well mention Morrowind and the Baldur’s Gate series (before 3, obviously), which he won’t reach for a long time but has been known to hold up as solid examples of the genre. Personally I still think Baldur’s Gate 2 is great. I’m also a big fan of the quest for glory series, which crpgaddict has rated, but might not make his list of top scoring RPGs, because they’re a hybrid adventure/RPG, so not all of their strengths appear on a scale designed for pure RPGs.
As someone who didn’t play them back in the day, I feel like SotN holds up but Super Metroid doesn’t. Just as another opinion. I couldn’t really get into metroid fusion either. To me it feels like the moment-to-moment action gameplay is too clunky in the early metroid games I’ve played, even if the exploration element is neat. I did enjoy playing SotN for the first time a couple of years ago though. It’s been a while since I played either, so they’re not totally fresh in my memory - I guess it’s possible that I’m just more forgiving of clunky melee combat than clunky shooting.
Tangentially related, always amuses me how “metroidvania” has become the genre name, when originally it was just a way that reviewers poked fun at the big change between SotN and earlier castlevanias. They were like “this isn’t what I expect from a castlevania, it’s a great game but maybe they should have named it metroidvania”, and the name stuck. Another odd fact about that terminology is that according to interviews, the SotN designer never played metroid - they were inspired by the non-linear exploration with different routes opened up by items/upgrades in Zelda games (although obviously adding that to castlevania’s platformer gameplay makes it more closely resemble metroid). So it should probably be considered a zeldavania.
Talking to people and examining writing will usually drop references to a couple of other places to explore, or to unanswered questions that are worth looking into. Even if they seem minor, these almost inevitably lead to putting together pieces of the larger story, regardless of which pieces you start with. I don’t specifically remember what whistling guy talks about, but it sounds like that’s the only potential lead you’ve found so far. It’s certainly possible to make progress without ever talking to him, via all kinds of things that can be independently stumbled on, but if you haven’t found anything else I bet revisiting his dialogue will give you an idea on where to search next.
(Okay, I checked the wiki and can confirm that, while Esker is not the richest source of new options in the game, his dialogue does include instructions that lead to new threads for you to pull on)
Where have you visited so far? Usually I’d think you’ve encountered something other than the ship within a few hours, and most of the things you can encounter should give you ideas as to what else to explore. Have you literally only floated around in the ship, or is that a way of saying that the things you’ve found aren’t interesting to you?