To me, the #1 re-release spot goes to Rez Infinite. I love KH Final Mixes and some SMT ones as well but I guess those are updates?
However, for Rez Infinite, it's not the standard game itself that was better, but rather the VR mode. They added a new bonus campaign (Area X) specifically designed for VR, which was cool, but the original game was also ported to VR. If we're talking remake/remaster, this is my favorite one. The new VR mode of the original campaign feels like the definitive version of it. It's as if the game had always meant to be played that way, even back on the Dreamcast and PS2 in 2001. Rez was designed to be like an acid trip, the VR mode accentuates this times a million.
That's why I think it's the best re-release of a game ever: it's essentially the same game, the vision stays intact and the intended artistic expression conveyed by the game remains unchanged but it's now made better, WAY better, through technology that wasn't there at the time. It's like Tetsuya Mizuguchi (game's main creator) meant for the game to be VR without really knowing what that was, since it didn't really exist, and realized "oh hey, I can make the game I envisioned now" when it became a thing. Rare example of a game that was ahead of its time not because of its impressive technical feats, but rather those it simply could never achieve back when it released. Glad it got the treatment it deserved.