I didn't like ST. Trains don't fit Zelda; they seem too modern world somehow; out of place in a way for a fantasy setting. The Spirit Flute was annoying. I have carpal tunnel and my wrist can stand much strain. And for some reason when I had to play the Spirit Flute it would put a slight strain on my wrist; probably from having to blow into the mic just right and move the flute with the stylus at the same time. The mic on my DS is temperamental and I have to blow into it just right for things in the game to register correctly. And though I don't have asthma I do get short of breath easily and all that blowing, for the Spirit Flute and the pinwheel, is a bit hard on me. Final battle was definitely disappointing for me. The credits were pretty though.
PH on the other hand, more sailing like in TWW(I always did like the sailing though I heard that some people didn't). No more of a limit on your cannon. Easier to aim with the cannon(though no matter what I still have poor aim). OoT/MM style fairies. I had missed those fairies; Ciela amused me. And I loved Linebeck. So good at comedy relief, and surprisingly deep despite that. Fishing sidequest. Fishing on the sea was interesting. And, luckily for me, not much use of the mic in the way of blowing. Yes, I will admit that the back-tracking was annoying. But for some reason I liked seeing if I could beat my time in ToTOK(For some reason whenever I'm in there the theme from Mission: Impossible starts playing in my head. Must be that whole stealth thing.) And I always enjoy searching for treasure.
So yeah, I also loved PH but hated ST.