Either because they were bloody hard or took ages or whatever.
Golden Sun: The Lost Age
I frequently was either lost/had no idea where to go next. It was pretty long too and required a lot of time dedicated to it. The final boss took me ages too.
Zelda: A Link to the Past
I found it frustratingly hard.
Zelda: Majora's Mask
The save/time system put many people off and prevented them from completing it, and I too went through a period where I left it for a while, but I managed to get back and stick to it and complete it.