They are different because they are increasingly more powerful hardware, Twilight Princess has a whole sword Fighting system and the Wolf form mechanic that is a huge change to Ocarina. There is a clear focus on exploring the map, but one is on the N64 and the other is on the GCN so obviously the scope and the mechanics are more simplified.
Sequels don't have to be the exact same game with better graphics, Persona 2 and Persona 3 play completely different and they are considered Sequels to each other. Resident Evil 4 plays differently to RE Code Veronica and RE3, nobody would call it a spin off.
Fallout Tactics is explicitly considered a spin off by the developers of the original. Breath of the Wild is contantly refered to as "The latest entry into the Zelda series" and it's the mainline game. No idea why you are insisting on this "It's a spin off" angle to be honest, truly baffles me.