Fridge Logic: Why does Bowser Jr. keep screwing time waiting for Mario to beat each world boss to drag Peach to the next world when he could just run all the way to the last castle without wasting time?
Game Breaker: Against bosses, the Mega Mushroom will destroy ANYTHING. Even Bowser.
Power-Up Letdown: The Mega Mushroom looks awesome, but if you break a pipe, you can't go down it, ruining your chances of potentially finding a Star Coin. Also, the Blue Shell handles awkwardly with its sliding mechanic, though it does improve your swimming. The Mini Mushroom, meanwhile, lets you jump higher and with (much) floatier physics, as well as access certain areas otherwise inaccessible, with the drawback that it has zero hit points; one hit from anything will kill you. When you're going for all the Star Coins and have to use it in the later levels where things get hectic...all those lives you accumulated in the early levels are going to come in handy.
8-6. Vertical level with lava rising constantly. And the midway point appears early in the level.
8-Tower 2. This one has you riding a snake block with almost all the way. But there are so many obstacles in the way, and it can particularly get annoying when you are trying to grab all three star coins. Of course, you have to ride the snake block, or else you will die.
Underused Game Mechanic: The Blue Shell is fun to use due to its defensive capabilities and shell slide (also, nice to have the Blue Shell not be the object of fear and hatred for a change), but it appears far too infrequently (while there is an enemy that drops it, said enemy only appears in a multiplayer stage), and none of the stages are really built around using it. It's also one of the few powerups that hasn't appeared in any other New series games, though the Penguin Suit is a Suspiciously Similar Substitute.
Win Back the Crowd: Up until the release of New Super Mario Bros., 2D platforming games were mostly relegated to indie PC games. With console gaming, platformers in general were starting to fall out of fashion. 2D platformers were all but dead and the number of 3D platformers considerably shrunk. NSMB was such an unexpected success that Nintendo decided to release a Wii sequel. That one was also a huge commercial success and led to 2D platformers returning to the mainstream in the console market.