I believe that The Minish Cap and Skyward Sword both took up a significant amount of hours for me to complete. For SS, the game was just designed to last longer than previous installments. I was also playing the game blind the first (and only) time around, which made me more inclined to explore, take mental notes of suspicious areas, try to figure out what was next in a quest, and what items worked on what enemies. Plus, I got lost in every dungeon. I think that includes the first, but I cannot be entirely sure.
The Minish Cap is harder to understand. For one, getting all the figurines for a 100% run takes many an hour. The Kinstone fusions are difficult to find partners for, as multiple characters can all get the same results, so walkthroughs may not help much if you fused previously with a character it did not suggest, not to mention all the times I need to fuse, but was lacking the proper Kinstone. Because of those difficulties getting all the hidden pieces of heart was a pain, plus the one that you need from the girl that continuously loses her Cuccos. Under a standard playthrough, TMC would not take much time to beat at all, but my completion nature extended the process.