Train gameplay was actually enjoyable for me (especially the way it got used in one of the end game fights was so cool). It was also nice that Zelda was an actual part of the game and helped solve puzzles instead of some princess locked away in a castle.
I played Phantom Hourglass much later and Spirit Tracks honestly just felt much more polished and fun.
I really think that everyone really had trouble with the DS microphone rather than the flute challenge itself. It came pretty easily to me but I doubt I'm a particularly expert mic blower, so I can only think my mic was a fully functioning one and people like you got a much harder challenge.