"I was the one who added the nuts to that statue!"
This whole concept of this game is screaming with Accidental Innuendo. The Bros are "inside of Bowser's body." They have to "stimulate" his body parts. If you have a dirty mind, you'll be snickering all throughout this game.
Especially hilarious when, finding Bowser's funny bone near the beginning of the game, Starlow overtly says "If we can stimulate this thing, something'll happen...". Now take it out of context and try not to grin...
Not to mention that to make Bowser giant-sized the Bros. have to play a mini-game ... in Bowser's rump.
The giant Piranha Plants. They're not actually blocking your path, as after you beat them, you land back on the ground and go a different way to get to where you need to go next. Their only purpose is to introduce the Chest Station mechanic.
Princess Peach's "Wish Power" at the beginning of the game, where all of a sudden she has the ability to telekinetically lift Bowser and throw him from her castle, something she has never shown capable of doing before (since such a power should make avoiding capture a lot easier) and hasn't been shown since.
Edges into Fridge Brilliance when you note that she was doing it along with the star based buddy of the game. She was just doing her standard 'end of game final boss wish power' she does very often but there was nothing to stop her from doing it right away.
Broken Base: Fans have mixed opinions over "Tough Guy Alert!", the regular boss theme. Some people enjoy it for being peppy and energetic, while others find it too cheerful, often citing Soundtrack Dissonance for the more pivotal bosses such as the Dark Star and Dark Fawful, and claim that the later boss themes in Dream Team and Paper Jam do a better job of alternating between fun and tension, on top of having at least a different boss theme for the penultimate boss (Antasma in Dream Team and both Bowsers in Paper Jam).
The Magic Window for the Brothers. It lasts until, and only until you screw up or every enemy is dead, and its damage would potentially be infinite if not for that pesky thing called "human reaction time," as the bros constantly speed up as the attack keeps going and the input window becomes more precise. Still, it can rack up more hits than any other move in the Bros' arsenal before its speed ramps up too much.
The Spin Pipe is less SP-expensive than the Magic Window, and fairly easy to do if you keep your eyes glued to the end of the pipe as it spins, and still positively devastating even in the final battles.
Magikoopa Mob or Koopa Corps. for Bowser. The latter especially since done perfectly, it will do damage comparable to even Broggy Bonker for less SP.
Mighty Meteor in the Gauntlet. It gives you more powerful items when used than the game means you to have available. Really useful vs Dark Star or Bowser X.
As far as gear combinations are concerned, DX SP Socks and a Budget Charm/Tight Belt on Mario gives you incredible special move usability, and the Delicious Gloves (Healing items are twice as effective) mean your opponent better kill you in one turn, or SUPER NUT! For Bowser, the Hunter Band is effectively a vampiric power-boosting item which can give up to a 30% attack bonus. It's pretty terrible against bosses, though.
The Intruder Fangs give Bowser two turns per round. Of course, you get them by getting Bowser to Level 40, and the game is usually finished at a much lower level, so by the time you receive them, you've probably already beat the game.
Bowser equipped with the King's Shell (his best armor which raises his defense greatly and his punching power by 30 percent) and his Intruder Fangs (which allow two actions every turn) combined with Broggy Bonker (his ultimate attack) being used both times makes the rest of the game into a joke.
The Giant Shell accessory. Its description says the wearer takes no damage from hits that do less than 20% damage than the wearer's overall HP. Problem is, most attacks in the game don't do that much damage with enough defense investment. Equip this on one of the brothers and you can ignore them for the rest of the game except when attacking with them. In fact, if your defense is high enough, you won't have to bother with defense increasing equipment.
Most bro-targeting attacks can be dealt with simply by dodging/countering with both Bros (as opposed to pressing the button of the brother being targeted). There are moves that explicitly punish this tactic, but only occasionally.
Fawful's line "Beef? I am lacking in beef. Fawful is beefless" becomes much funnier after Dream Team introduced the Massif Bros., who barely talk about anything else except beef.
Some fans were joking that the third Mario & Luigi game would be a "platformer"-like game, similar to Super Paper Mario, the third Paper Mario game. Well this game still has the 3rd Person mode, but inside Bowser, you get to experience it in a 2D aspect, similar to Super Paper Mario. This was passed onto Dream Team as well.
Ho Yay: Bowser locking his mouth on Midbus's snout and inhaling his breath for an extended period of time. True, Midbus was a frozen block of ice and Bowser was burning up inside after swallowing the Dark Star, but it was still hilarious. Though Bowser does say something to the effect of "That was gross" after doing it.
Idiot Plot: The plot revolves around Bowser putting suspicious things in his mouth. Twice.
Some of the Fawfulized enemies. Not only do they all sport his glasses and possibly-now-creepy smile, but there are also the implications that arise for Chain Chawfuls that you can liberate by getting rid of Fawful's influence instead of just beating them up like usual.
The Scrappy: Starlow gets quite a lot of hate for being an annoying Exposition Fairy. Even Bowser gets increasingly annoyed with her as the game goes on.
Not many people like the way you have to blow into the DS's mic in order to breathe fire during the Giant Bowser parts. This is especially frustrating in the battle against the Fawful Express, as this is the only attack you can do to hurt it since the train is too low to punch.
That one-off carrot minigame with the Wiggler in Dimble Wood, especially the fact that the screen-clearing enzyme appears in the carrot chunk that comes after the flash, rather than the one during.
The pollen minigame can also fall into this; the controls are finnicky, aiming the pollen into the correct section of the wall can be difficult, the blue pollen makes you drop coins, they are very frustrating to avoid and you can only get hit 3 times before you have to start all over again.
When Bowser's back is healing, you are told to wait for a while and come back later. Most people would close the DS and go do something else, but the DS goes into sleep mode when you close it, and sleep mode does not count time. You have to leave the DS open for about ten minutes (or punch in a code that can very easily be missed) to complete the task. The code is: A B X Y L R Y X B A
The Challenge Medal comes in the form of an Accessory item and must be equipped on a Bro in order for its effects to apply in the game, thus needlessly taking up a very valuable gear slot (which you would need that much more in said mode).
Surprisingly Improved Sequel: Bowser's Inside Story addressed complaints regarding Partners In Time, like changing special attacks back to the original system, making the controls less complicated, and adding the overworld back in, and did some other things like making Bowser a playable character and Fawful the main villain. It's largely regarded as the best game in the series, and became the best-reviewed and best-selling RPG in the Mario franchise.
Giant Bowser's fight against the Fawful Express. Not only are the attacks powerful and hard to dodge, but you have a limited amount of time to win the battle, or it's an instant death. Also you can only use your flame because the train is too low to punch, and you have to destroy several obstacles along the way, which is a big problem if your DS microphone is wonky. If you beat this on your first try, give yourself a pat on the back. If it took you a couple of tries to beat it, don't feel bad and just be happy it's over at last when you finally achieve your victory.
The Mario & Luigi fight between Memory M & Memory L. What makes these two bosses hard as that they seem to copy the Mario Bros.' statistics: Mario is more powerful, and Luigi has more HP. Mario's two attacks are quite frequent: one of them has him get a Super Star and become invincible, ramming through the Bros. (on some occasions, a coin will pop up and Memory M will follow it). His other attack is growing huge and breaking bricks so that the Mario Bros. have to break the remaining parts fully. Memory L's attacks appear less often but are scarier than Memory M's: One of them is throwing a hammer in the sky so that one of the Mario Bros. have to whack it back; the other one likely requires the most timing, as Memory L will get pursued by a Memory Boo: he'll jump over the players, but the Memory Boo won't. You want to know what's worse? If you defeat Memory M first, Memory L will simply revive him (thankfully only a little bit of HP, though). Because of this, you may think to defeat Memory L first so that he can't revive Memory M when defeated - but Memory L is just a coward as Luigi, and will often run off the battle screen, and will likely not return until Memory M is defeated. Get ready for the pain.
Junker. His first couple attacks aren't too hard to dodge - but then he sucks up Luigi and puts him in one of the Junker Cans. Now you have to use Mario to defeat the Junker Can containing Luigi, but Junker and his minions will use a wide variety of attacks to keep you from freeing Luigi - worse, if Mario is defeated while Luigi is still in one of the Junker Cans, the battle will instantly end. It doesn't help that his other attacks do pretty high damage as well...
They Wasted a Perfectly Good Plot: All of Giant Bowser's boss battles were with machines of some sort, but never against a giant Midbus. They could have worked in Fawful using the Dark Star to power him up to monstrous heights and gives us a bit of Godzilla homage.
Viewer Gender Confusion: It's mentioned twice, early in the gamenote "NOT how to treat a lady!", and during the Flab Zone quiz, that Starlow is a girl. Few people seem to remember this.
The Woobie: Bowser doesn't seem to catch a break in this game, losing his home and his minions to Fawful. He may be a Bad Boss but his minions all leave for some really petty reasons (mostly for money and food).