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.
In fact, the whole game can pretty much be summarized as a game full of fetish appeal, as shown in this post.
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.
After the Superstar Saga remake genericized several Toad NPCs to the point of undermining a joke with a female Toad, the March 2018 Nintendo Direct indicated that at least the important minor Toads such as the first Blorbed one would retain their looks for this game's remake.
As seen in Broken Base, there were people disappointed in the fact that Dark Fawful and Dark Star shared the same boss themes as everyone else. In the 3DS remake? Nope. Both endgame bosses have their own separate boss battle themes, and the former's is a dark remix of his and Cackletta's battle theme from the first game!
Additionally, in the September 13 2018 Direct, there's a portion during Bowser Jr's segment that there's three completely new and original characters (that end up being minions of Fawful nonetheless), something that was heavily criticized during Paper Jam.
Using the DS's microphone for Giant Battles is seen as a Scrappy Mechanic to many in the original game. The remake does away with this for the touch screen instead
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. At least until Dream Team. Just before the Final Boss against Dreamy Bowser.
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 (at least in the DS version), 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).
Whether or not the game needed a remake. Some say that the remake can stand on its own, providing a nice upgrade to the graphics and music, along with an improved sequel to Minion Quest in Bowser Jr.'s Journey. Others believe there's no real reason for the remake to exist, considering the original game isn't exactly rare and can also be played on 3DS, and believe that the sprites and music of the original are better.
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. Slightly Averted in the remake, as it stops after a time.
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.
The "Daredevil Mario" setup popularized by Skawo. It works similarly to the "Danger Mario" setup from the Paper Mario series, but with the added perk of being invincible. The Daredevil Boots are a piece of gear that massively increases attack power at the cost of being a One-Hit-Point Wonder. Mario, being a Glass Cannon already, is perfect for these due to his high attack. Now take the Gumption Socks, a piece of gear that allows the holder to Auto-Revive after a few turns without the use of a 1-Up Mushroom. Mario now has immense attack power both from his stats and the buff, and renders the One-Hit-Point Wonder issue a moot point due to being completely unkillable. Even when Mario's out of commission, Luigi's Stone Wall build will make sure that you have relatively little to worry about when defending him. The aforementioned Big Shell helps as it allows Luigi to soak up hits more easily when Mario is out.
Many of the enemies and features inside Bowser are cleverly named, such as Napse (synapses, connections in the brain) Emoglobin (hemoglobin, the compound that allows blood cells to carry oxygen,) and PEP (polypeptides.)
Incidentally, those are called Shinapun (a play on shinapusu, meaning synapse), Hemogurobin (hemoglobin) and Enajī (energy) respectively in the Japanese version.
Goddamned Boss: The fight with Fawful without a doubt. He's not a particularly hard boss, but only 2 of his attacks will let you hurt him, one of which qualifies for That One Attack. As a bonus, whatever damage you do will be healed almost immediately by his vacuum helmet, which can't be attacked by Bowser. What you're supposed to do is wait for the helmet to detach from Fawful and inhale it so Mario and Luigi can destroy it. The problem is that Fawful will take his sweet time before it happens. And when you finally get down to fighting the helmet, it just loves to steal your special attacks. It also enjoys stealing your items so you can't replenish your BP. Be prepared to wait for absurd amounts of time for the fight to go anywhere. The remake alleviates this issue somewhat, as Bowser's special attacks can hit the helmet while it's on the field.
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. Then in the remake of Bowser's Inside Story, we're introduced to three new characters working for Fawful... and one of them is called, you guessed it, 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 3D 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.
All bosses (and Bowser on occasion) gain the Fury status ailment past a certain health threshold. This includes Fawful. After seven games, Fawful actually DOES have fury!
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. Technically three times, if you count him involuntarily swallowing the Dark Star. And 4 times if you also count what happens at the end of the remake's side story.
Jerkass 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).
"It is I who nuts to that" Explanation A cropped picture of Fawful's quote upon seeing Bowser at the Sea Pipe Statue; "It is I who added the nuts to that statue!" It's generally used for reacting to a NSFW/sexy thing on the internet.
"It is I who nuts to that" HD Remaster Explanation Once it was discovered that the Fawful quote the original meme was derived from was completely intact and had its text wrapped in the same way as the original game, it took no time at all for the Bowser's Inside Story + Bowser Jr.'s Journey version of the meme to see creation and circulation.
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.
Peach's Castle, but of the more 'unnerving' flavor. After Bowser Castle, you might expect Fawful's takeover to be relatively lighthearted. But once you pass the Dark Star blockade, you find that the castle's been completely overrun with Fawful's Elite Mooks, not a friendly face in sight (other than the three Paratroopas), with several of the enemies on the inside having been tainted with the Dark Star's power. And the courtyard even has this eerie music.
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. The remake doesn't use the microphone on the 3DS, as it uses the touch screen for the attack now.
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. For those wondering, the code it 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). The remake, however, takes an odd approach at fixing this issue: it essentially turns it into something that basically turns the Bro you equip it on into a Glass Cannon.
Junker's Thwomp attack. Jumping at the right time to avoid the falling Thwomp is tricky, and if you happen to get hit by the Thwomp, you could get dizzy and be unable to attack for a while.
Junker also has his suction attack. It can't be avoided (in the original; in the remake you can button mash to get away) and traps Luigi in one of Junker's minions, disabling him and the use of Bros Attacks. Further, if Mario falls while Luigi is trapped, it's Game Over. Mario can free Luigi by defeating the minion holding him, but said minions periodically switches which one holds Luigi, making it that much more difficult to free him (though there is a chance that the minions fail to catch Luigi when switching him, freeing him early).
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. The only thing saving him from being harder than the other bosses is his really low Defense, meaning you can potentially finish him off before he can suck up Luigi if you've played through the game killing everything in sight. The remake thankfully makes this a lot easier by allowing Luigi to avoid the suction altogether if the player mashes buttons hard enough.
Believe it or not, Durmite, of all bosses, manages to be a complete pain in the remake. Both of her attacks are much more erratic and still deal somewhat high damage, especially her string shot attack. If you don't have the reaction time of a professional sports player, and if she chooses to swing her string at Mario first, expect Mario to lose a good chunk of his health. And if she uses her straw right after she knocks out Mario, she basically gets a free turn to restore some of her HP due to Luigi's crappy Power stat.
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 a Godzilla homage.
Tough Act to Follow: Bowser's Inside Story is considered one of the best RPGs in the franchise for its hilarious yet engaging plot and its gameplay striking a balance between simplicity and intricacy. Its reception even rivals Superstar Saga and Paper Mario: The Thousand-Year Door. Many fans agree that Dream Team and Paper Jam don't measure up as sequels for various reasons.
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.