Favorites: It's a tie between TP, WW, and ALBW. Both TP and WW have amazing stories, and both have great dungeons, with TP edging over WW in dungeons, and WW edging over TP in overworld. They both encapsulate what I love about 3D Zelda. ALBW is the opposite, I wasn't amazed by it at first, due to it's more simplistic story line, and simpler dungeons, but it does still encapsulate what I love about 2D Zelda.
Least Favorite: This is a tie between FS (not FSA) and TFH. FS is incredibly simplistic and is focused solely upon shorter levels with very simplistic dungeons to compensate for the single player mode, thus when I played it for the first time on the DSi in the anniversary version, I found it lacking, even though I really loved the retro levels. TFH, I haven't played, but I might one day as I'm not against giving it a chance, and I love exploring different areas outside of Hyrule, and I don't even mind that the Kingdom is obsessed over fashion. What I do mind though is the story, the way Link is handled which abhorrent, and the near lack of any real thought put behind the single player mode.
To start, the story, it just sucks, and it could have been fixed quite easily. To explain imagine if it was laid out like this instead: instead of the Princess being cursed to wear a "fashion disaster" she should have instead been forced to wear a suit of evil magic that was solely zapping her energy and was a threat to her life, and this should have been done by the witch who should have been possessed by some evil spirit in hopes of using her natural fashion skills to slowly conquer Hytopia. Likewise, the game should have started with a prologue that showed Link on his way to Hytopia, only to bump into the witch, as she's fleeing from having cursed the princess, and in a rush and to prevent Link from stopping her, the game should have had it so the witch split Link into three to split his power, then fade to black and have 1/3 of the Links show up in Hytopia. This would have made the story a touch more serious, and it would have made sense of Link being there, instead of there just apparently being a billion Links running about. Gameplay wise, you should have just naturally have been controlling three real Links in the Drablands regardless of if you were playing multiplayer or single player, and there should have been a toggle system to have automatic lineups similar to FSA. This I think would have made the game better. All that's really left about the game other than the story and the Link issue and the gameplay issues, is the dresses, but I don't like those for my own reasons, and they're not necessary a problem.