The Legend of Heroes: Trails in the Sky (Part 1 + 2) are really the first ones that come to mind for me. They reignited some of the feeling of excitement I have for JRPGs, where you become deeply invested in the struggles of the characters and enjoy every last "Big damn heroes" moment and sudden twist they pull out. The villains in those games are pathetically irredeemable, a far cry from some of the better written ones, but their amazing quality is in forcing out the most dramatic possible circumstances from the characters. Combat keeps its pace and was generally enjoyable for me, plus it had an XP catchup/slowdown system that stopped the game from ever feeling too grindy.

Funny thing is, I personally bear no recommendations for any games in that series beyond those two. They are, to my mind, a testament to good singular stories that leave the opportunity for future ones - even if those follow-ons didn't click with me.

For Metroidvania style, Aquaria is one I don't see mentioned much. I got it in one of the classic Humble Bundles, and it had a LOT more content than I was expecting for an indie game. Many different abilities to gather, a soundtrack and appearance that all blended together so well, and even optional bosses hidden in the waters.

And then, it comes up every so often to divisive opinions, but there's plenty of shooter players that still need to try Spec Ops: The Line. It's not terribly well-done in terms of gameplay, but tells a very compelling story about heroism and violence - even if it is NOT the one you hope to see. Much of the controversy over the game's ranking has to do with how much it offers freedom of choice - but I've always felt that freedom of choice starts in the type of adventures you choose to play. You see the assault rifles on the cover. You're planning for this.