I think this is a game that is like, quintessentially more than the sum of its parts. I can point out a hundred things wrong with the game, but for each of them I feel like it's counteracted by just... the overwhelming impression that the game leaves on you. The last game that made me feel this way was Actraiser, which is actually one of my favourite games of all time.
The strongest thing about the game is just how much thought went into the game world. Hillys is small and there isn't very much in it--actually, it's almost comically tiny in scope--but everything in it was thought through so well. Every character feels like they've been individually placed and given life and a daily routine. Pey'J, Jade, and Double-H are so well characterized, but so is everyone else--I especially loved the Rasta Rhinos at Mammago garage. There's a strong sense in each and every character interaction that these people are part of a shared world that existed long before the game started. There are only 3 dungeons, but each has a very strong sense of purpose and layout and central mechanics. The only real item upgrades you get serve very obvious purposes. It's a breathtaking economy for a game.
Even something like the spiral keyboard interface is basically totally irrelevant--there's no reason why you couldn't just push a button once you got the access code instead of entering a password... but it was so well thought out. There's basically no chance your team members will die, and yet the game has a unique, never-before-seen mechanic where you can basically change your health allocation between Jade and the sidekicks. Every time the game introduces a new idea, it works, and in most cases, it's never been done before.
One thing I wanted to note is that I love the way the game de-activates the combat mechanics in every area where they're not needed. It gives the strong impression that combat is a secondary part of the game rather than primary, which is very refreshing in comparison to most games.
In contrast to many others, I don't think the game needs a sequel. I mean, if someone were to do a newer game with the same driving philosophies as Beyond Good & Evil, that would be great, but I think the game stands very well as a self-contained work. We know the recent history of Hillys, the players in this urgent moment of the planet's history, and the antagonists. That the DomZ are not fully defeated or that the Jade / Shauni plot is not fully expanded on is kind of irrelevant. I feel like the game stands on its own like A New Hope does. Vader didn't die and the Empire didn't collapse, but the good guys get a big win and we're left like we had a glimpse into such a pivotal moment in the struggle. The Pey'J cutscene at the end of the credits is an unfortunate tease, but that can easily be set aside.
Really wonderful game and well deserving of its place in the canon of great games. It'd definitely make my Top 100.