These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Game Breaker: Copy Flowers and Trampolines. The general idea of both is the same: with proper timing for the actions commands, it's possible to deal stupidly large amounts of damage to enemies with one use. Add to that the Ulti-free Badge, which gives you unlimited Bros. Items for that character.
Goddamned Bats: Shroids. They have one attack that is very annoying. It takes two flags, and the bros must jump/do nothing depending on color raised, performs this multiple times (up to six), and one failure results in an unavoidable attack. Also, it may summon a UFO that drops a spikeball, countering this causes the Shroid to malfunction. This means the "flag" attack from earlier is reversed- the other brother needs to jump for each flag raise. Fun.
The Toads in Toadwood Forest have the life (known as vim) sucked out of them, which is later used to power up the Shroob saucers. The vim sucked from the Toads has the appearance of green liquid with images of sad Toad spirits inside it. Although this is likely not the case, given the ending, the spirit images have led some to believe that they are the souls of the Toads, sucked out by the Shroobs.
Yoob, who eats every Yoshi it encounters in sight (and later the Mario Bros and Baby Bowser), which are later encased in eggs which would most likely make more Yoobs to help conquer the Mushroom Kingdom.
Inside Yoob, you can see him wince in pain when the Babies use the hammer or the Baby Drill. The latter is especially wince-worthy if you consider that Yoob just had something drilling into his flesh and is moving underneath it.
The Shroobs' destruction of Toad Town, Peach's Castle, and Hollijolli Village, none of which even stood a chance of defending themselves.
Padding: Bosses having far too much HP. This was notably only done in the American version, with the European and Japanese versions (which actually came out after the American version) being more reasonable. For example, Princess Shroob has 1700 HP in the Japanese version, because they knew a boss constantly protecting herself with a barrier did NOT need 3000 HP.
The Scrappy: The Stargate gets a lot of hate for being an unreasonable Jerkass to Luigi. Even though he later admits that he was only doing it to see if Mario would defend him, his cruelty to justLuigi (i.e. giving him three options to answer a question, calling them all wrong, declaring the answer an unavailable fourth option, and accusing Luigi of lying when he points out that said fourth option did not exist for him to pick) rubbed fans the wrong way.
Sophomore Slump: Many fans consider this game weaker than Superstar Saga, due to the fully explorable world being replaced with a more linear set-up and due to the controls getting a little convoluted what with all the switching back and forth between A/B and X/Y. Probably the reason Bowser's Inside Story returned to the explorable world and kept the A/B and X/Y portions completely separate.
The humor also seems lazier, mostly content to hurt Luigi.
Squick: There's an organic structure leaking water like a fountain inside Yoob's lower gastrointestinal system that you need to make Baby Mario drink from. This doesn't go unnoticed in the official strategy guide, which refers to it as "delicious Yoob water".
That One Boss: The battle against Bowser and his younger self is surprisingly difficult compared to the previous bosses, since their attacks are somewhat difficult to dodge, they utilize combination attacks with several fake outs, and they hit HARD.
Also, Petey Piranha, while not as hard as the battle in Thwomp Volcano, switches between being flying and spiked and takes some time to learn the tell for his flying attacks. Also, he's one of only three bosses in the game who is only one target to attack multiple times a turn. It should be noted that the Bowsers and Petey are the two Climax Bosses.
That One Level: Gritzy Caves is a rather long level filled with minigames and whatnot.
The Woobie: Peach. It's one thing to have Bowser kidnap her knowing Mario will routinely rescue her, but here a hostile alien race doesn't have the same concern for her as Bowser to keep her unharmed, at one point feeding her to Petey Piranha for a quick laugh. Also, while Bowser would only storm into her castle and kidnap her, the Shroobs are the first antagonists to attack her entire kingdom, and she's powerless to stop them.
Woolseyism: Let's face it, would this game really have the Hammer Bros. talking in 1337 in the Japanese version, saying things like "ROFL" or "PWN"? note In the Japanese version, they speak entirely in katakana. But unlike in Japanese, where one of the purposes of katakana is to be robot/cyborg language, in English, it is considered highly cliché and unimaginative to have ROBOTS OR CYBORGS ALWAYS SPEAK IN ALL CAPS LIKE THIS WITH NO OTHER VERBAL TIC IN THEIR SPEECH.