I agree with you completely. Well I can't say that I "loved" Phantom Hourglass, I did quite enjoy it, and found it a fun game to play. I actually didn't mind the controls that much, and even enjoyed the Temple of the Ocean King to a certain extent, especially once you've finished the game. Finish the TotOC with a full 20:00 minutes left on the hourglass was pretty fun. However, I really didn't like Spirit Tracks. I simply found the game incredibly boring. In fact, I got so bored with it near the end that I never even finished it. Now, I was really excited for this game in the days and months leading to it's release, and while I enjoyed it for the first little while, I quickly became quite bored.
Even though riding the train was about as restrictive as the boat in Phantom Hourglass, I still really didn't like it. The escort and fetch-quest side quests did little to make the game more interesting/last longer, as they were incredibly boring. I especially hated giving people rides places, because of the fact that you had to travel even SLOWER, and obey all of the silly signs. The game just wasn't very fun for me.