There are plenty of issues that I see.
The writing is good, but there are no real companions to speak of (except Olivia, who is with you for the entire game, but she's the player analogue more or less). Every last thing is spelled out for you, and problems are solved within half an hour of happening upon them. Also Olivia is naïve to the point of retardation. Yes, there's a reason for that, but it seems like she hasn't learned a thing during the entirety of the game, and that's frustrating.
There are probably upwards of 500 Toads to save throughout the story, and they make up 99% of the population in the game. Remember how varied the starting town in Thousand Year Door was? Replace all of the residents with Toads and you've got this. Though, it *is* called Toad Town, but that's barely an excuse.
The battle system has a multitude of problems too. It's timed, for one thing. You have, like in Sticker Star (a game I didn't finish), weapons that break after a few uses, in addition to your regular jump and hammer, effectively making your standard attacks useless in the late game but they can't be swapped out - which would have been fine if the game let you have the weapons forever. It's also incredibly boring, and the last few fights I've just either avoided or used the Toad buyout to solve it so I can get on with the game. There's no incentive to fight random enemies, as you only get coins. And when you get a heart container to have more max health, that's when you "level up" your damage, but there's no way of telling how much, or see any other stats.
It's a mess, and it's frustrating because I see hints of something great at times, but it's overshadowed by this monolith of boredom that is the core gameplay.