Sitting here I am not sure. It would have to be something I play to relax or just chill with which immediately means skateboard games and motorcross games with free roam. None of the other alternative extreme sports do much for me here, even if I do like them -- some of the BMX games do well but I have never found controls I like which also detracts from the level for me.
Skateboarding then more or less means mainstream Tony Hawk (don't think we need the Disney spinoffs) or EA's Skate games. Skate 2's level was probably the best as 3... I like it and play it to this day but eh.
Shooting game wise. 007 Nightfire probably has some things to teach us here.
Platformer. Rare had some good stuff for the N64 but nothing I especially want to note in this. 2d wise then I do actually really like megadrive Sonic.
Open world. Morrowind is most likely my pick for Elder Scrolls but I dare say I would sooner do some of the later might and magic games, have not done enough Far Cry games right now to say and most of those are soured a bit by changing games and mechanics within the game (by the time you unlock stuf and clear out the bases the fun of exploration goes way down). Never particularly had any Japanese offerings do much for me, and dungeon crawlers are commonly both random and forgettable even when they are scripted.
All this is to say I am going to have to go think about this one. Did take a look at my wall of games and still have minimal.
Super Mario Sunshine has the best 3D Mario controls. fite mii
While I could see Mario Sunshine being best 3d Mario (though I would probably say it is) being a contentious pick I am not sure the controls thing would be.
Your competition/lineup is then
Some handheld efforts. Not going to happen so we can skip that. Some do impressively well with what they have but otherwise no.
Mario 64. A commendable effort but single stick and still learning the concept means it is unlikely to get too far here.
Sunshine. So conventional 3d by the time 3d was more or less figured out with a twin stick controller as standard (never tried a RE chainsaw controller here). Fludd makes things more forgiving but that is not a bad thing. Worst part is probably going to be climbing under the city as I always seem to forget the controls and release to my doom. No fludd sections are also really tight.
Mario Galaxy and its sequel. Probably as good as a wiimote ever felt for me but the planet gimmick got old very quickly. Can you even play these with classic controls?
Wii U didn't have anything 3d.
Odyssey then. Between the hat gimmick meaning most things barely made an appearance (though I will note the Sunshine roller coaster section also being fairly brief here, even if it was one of my favourite parts) and switch controls not being as comfortable as a dedicated controller (haven't tried odyssey with any kind of controller adapter).
Luigi's mansion would be next.
Don't know what goes for the emulated versions of 64. I will be interested to see what becomes of the N64 source recreation here.