No, it's currently #3. My favourites are LttP and MM, they're both #1 for me. For better comparability, let's stick to MM now: OoT really made the hugest leap gameplay- and graphics-wise and introduced a gameplay style that is basically still present in all following 3D Zeldas (only SS made the next major step while still relying on some of OoT's concepts like Z-targeting). Therefore it set a strong foundation for the future. But I think that MM improved over it in almost every aspect, I think that both the overworld (esp. Termina Field and Clock Town) and the dungeons were designed much better and with more detail. Also the graphics looked improved even though it was on the same console. And I liked how it didn't have such long tutorial parts like OoT did, you could start right off! Of course it also was more challenging and had better NPCs and sidequests. I think that MM is to OoT what aLttP is to LoZ: While aLttP perfected what LoZ started in the 2D world, MM did the same with 3D Zelda. Unfortunately it went a bit downhill with WW and TP (still good games of course)...