That awkward mechanic in Spirit Tracks grew on me. I'm actually enjoying it so far. It's got great puzzles, a lovely personality, and I even like the train sections of it. The only part of that that turns me are those possessed trains, as the only challenge it provides is delaying your trip because it forces you to make detours.
I'm not sure if I will call this a great game no matter what happens though because the use of the microphone is absolutely abysmal. But, I am playing it on the Wii U, so the mic is very close to where your hand holding the stylus is, and it's a challenge to even see what you're doing while using the mic. Perhaps it's easier on the DS?