3) Many segments of game progression are locked behind invisible blocks and narrow passages in the background of the screen. It's okay to hide extra, fun goodies and secrets to games. It's not okay to hide game progression behind those things. It's a puzzle to decipher hieroglyphics in a temple. It's not a puzzle to jump at a specific spot (and this is outside of the invis blocks that have flowers underneath them as a clue) or walk behind a random bush that otherwise looks flat, even with 3D on. Imagine if you couldn't clear the original Super Mario Bros without knowing where the invisible 1-Up mushroom was on stage 1-1.
4) There is no meaningful reward for combat; therefore, there is no reason to get into combat. Prior to world 4, the amount of coins you get for defeating an enemy is negligible, especially when stickers are so abundant that the only thing you need to use coins on is black market Things and secret doors. The one saving grace of game design in this aspect is that battles aren't forced.
I'm only on the World 2 boss right now, but I disagree with 3. I love the challenge of figuring out secrets, as long as they're not too hidden and are accessible. I've only had one problem with this on W2-4 with the oasis and the jar. I wasted a lot of things trying, then it turns out I had to go to a level I've never really been to before. Since I'm only on world 2 (I've progressed somewhat through 3) I don't know how the game handles the secrets after world 3, but I love the way they hide things.
I also agree with 4, I find myself just running from battles often because I'm almost out of hammers or jumps/etc. You get little coins from battles which doesn't matter because I've got over 2000 coins and I don't need anymore (for the time being.) This is where an RPG system would have come in handy, I think. Or maybe a system where every time you beat a battle, you get points that you could turn in at a shop for coins or stickers and whatever else I'm missing.
I can't really comment on 1 and 2 since I haven't gotten that far into the game yet, but I really like the game so far.