Problem is that NES Zeldas are not that well remembered. You have also to take into account the huge player drain Nintendo had during Playstation 1 era and many players who did not return to Nintendo never got a chance to play the 3d games.
One reason I choose the 2d games, especially the NES ones. 3d games took a very long time to put the player into action and I never liked them. One reason I switched to Falcom Action RPGs, especially Ys, that have more in common with NES Zeldas
For 3D zelda I do agree with some, at least for OoT, control issues aside OoT is good for an N64 game, which is why it did so well in the region that actually brought the N64, however it really was very bland and got worse the further you got in the game, backtracking across unlikely towns and fields, and performance issues. made it a turn-off. Among several other problems that were given a "pass" back then.
Majoras Mask tried to change that by having a real more atmospheric and interactive world. However, I believe majors mask should have moved development to the GameCube instead of being released on the N64 as, while they did a good job given the hardware, the N64 was still way to weak and too many compromise were made.
The first real Zelda 3D game that seemed to be made with the vision in mind was Twilight Princess since the Wii was basically a GameCube and it was a cross-gen release, so the hardware was taken into account and they were able to be ambitious without as many compromises, which is why the game is often highly regarded. Sadly they went back to compromising visions with Skyward Sword which should have been a Wii U launch title but what can you do.