It honestly depends on what I'm doing in the game. If I'm powering through the dungeons and just trying to get to a certain point in the game or complete the game I would pick warping. If i'm leisurely play and just enjoying my Zelda time then Epona, definitely. If it is my first play through of the game then it is just walking. I want to see everything there is to see in a new game, find the hidden caves/holes and secrets. If I had to pick an overall, I would pick WolfLink from TP. It is the combination of all of these modes of transportation. I can walk, run/gallop, or warp. In fact, I think that TP had the best transportation system of all the games. You had so many options: wolf, warp, epona, walk. It was fantastic.
As to the loftwing situation. I didn't enjoy it. It wasn't that I disliked it, don't get me wrong. But I thought it was rather boring you had to just glide until you go to the place you wanted to be. My biggest complaint has already been stated though. I really didn't like that it was confined to Skyloft. If all the areas had been accessible to each other and you could fly above them and drop kinda wherever you wanted to I would have liked it better. But really the major issue was the lack of places to visit in Skyloft via loftwing. The chests were the main attraction and they were one time deals. a couple minigames and a bar and beyond that...octorocks. To be completely honest my favourite part of fly on the loftwing was the training exercise where you had to break the targets. Beyond that, I didn't really care for it.