I recently picked my Spirit Tracks game back up and I have a couple gripes, some of which have bothered me in all Zelda titles:
The Sand Wand is annoying as hell to use, and it doesn't help that it's also a factor in something I've always quarreled with in Zelda games: not being able to figure out a puzzle because of something physically akward; especially when I've tried doing what I was ultimately suopposed to several times.
Now for the most part, Zelda games have fluent enough controls that puzzles are solved at least 98% with your brain and only a small bit of physical work. Pushing a block counts as a physical thing, but it's not like many Zelda puzzles require you to do acrobatic maneuvers. There was a part in Minish Cap I got stuck at because after trying several times to jump with a bomb across a gap, I kept falling to my death. After looking it up online I found out... I was supposed to do exactly what I was doing, just with a slightly different combination of buttons/timing. With the Sand Wand, I kept trying to get Link on the sand, but I just couldn't get it under him. Lo and behold, this was because the large pen I was using in lieu of my lost stylus wasn't apt for this task. Once again, an online video showed me that I had exactly the right idea with slightly bad execution. Don't get me started on the boss.
Once I beat the Sand Temple, and went back to the Spirit Temple, there was a dark room in which Spirit Zelda told me "look Link, a dark room! Let's just do what we did last time." Now, I'm not really stuck at this point, but c'mon Zelda Spirit, I haven't played this in literally 3 months, telling me to remember what we did last time is not very helpful.
And now I'm onto a puzzle involving a timer. This isn't Zelda-specific (unless we're talking about Majora's Mask) but just... fuck timers.
SPOILER ALERT VIDEO