The Hammerhead Bros.' But Thou Must! attitude towards their Hammer tutorial, complete with pretending to allow you to skip it and then coming back, can really make them come across as this.
The Koopa Troopa that teaches Mario and Luigi how to fight as a pair pulls a similar tutorial skip fakeout. If you decline the tutorial, he pretty much says, "Okay, but if you get beaten due to your ignorance, it would be all your fault." Once you get to a mandatory fight against a Goomba, however, the Koopa suddenly reappears and gives you the tutorial anyway, claiming that Bowser would get upset with him if he doesn't.
Any forced tutorials are removed from the remake, thanks to the addition of the guide mechanic from Mario & Luigi: Paper Jam. Now new players can simply view tutorials on their own time, while familiar players who already know the mechanics can skip it entirely.
The remake makes Bowser less of a Butt-Monkey, features the Minion Quest mode where his minions work to save him, and shows he's just fine in the ending.
As it is now required for 100% Completion, the switch in Joke's End mentioned in That One Sidequest below is now easier to get thanks to a new barrel accessible to both Bros closer to the switch, as well as being able to walk faster while Luigi is in a barrel.
Hammer guard in the remake holds as long as needed, whereas in the original it only lasted for a short time before the bro would drop his hammer and be vulnerable. That mechanic would be particularly frustrating for players who couldn't get the timing on an enemy's attack right.
Base-Breaking Character: Bowser has become this in hindsight, thanks to his more badass and competent appearances in Bowser's Inside Story, Dream Team and Paper Jam. Superstar Saga is arguably the Mario game that shows Bowser at his most patheticnote along with Mario Party 3, as he spends most of the game either as an amnesiac sidekick to Popple or a passive vessel for Cackletta, all while being kicked around by the universe and not having a single boss fight as himself other than the tutorial fight. As such, fans of Bowser's later appearances tend to dislike how he was portrayed in this game, while other fans find his comic relief antics amusing and enjoy his Butt-Monkey role across the RPGs. Some in the latter camp argue that if Bowser wasn't benched in the story, then there wouldn't be as much focus on the other villains, and Superstar Saga was one of the very few Mario games at the time not to have Bowser as a main villain.
Superstar Saga is highly beloved, so the remake caused some breakage. Many fans were disappointed by the design standardization, feeling that the game's Early Installment Weirdness with regards to character designs was one of its major charm points and that it feels soulless without them. They also dislike the removal of some unique NPCs and the Geno cameo (not helped by this game coming out after several Mario RPGs where Nintendo didn't include any truly new characters), and it uses the still-contested graphical style of Dream Team and Paper Jam. Other fans are just happy to see an RPG as unique as Superstar Saga getting attention during the Dork Age of Mario RPGs, enjoying the updated graphics and seeing the redesigns and removals as a consequence of time passing or a way of tying it in with the rest of the series.
The remake's soundtrack also has mixed opinions from the fanbase. Some see it as a way of Yoko Shimomura losing her touch, as some songs either downplay some of the instruments of the song (the final boss theme for example) or is simply just not as good as the original. Others, however, believe that the OST is better than the original due to the 3DS' superior sound chip and enjoy the different takes on the soundtrack.
Clumphs. They've got massive HP and generally come in pairs, making for a very long fight. And they're no slouches in the power department either, as they sport one of the biggest non-boss attack stats in the game. They can be instantly defeated by Mario's Firebrand, but it's random and you got no experience by doing it. Even worse? They're Joke's End enemies, meaning you must battle them alone along with the other monsters in the zone. And if you're controlling Luigi (who has the Thunderhand ability instead of Firebrand, meaning no instant defeat with him), prepare for a lot of pain.
The Gunner Guys in The Very Definitely Final Dungeon. They only have one attack, but it comes in two varieties and it's hard to determine how it will attack you. And if they hit you, you will not only take a lot of damage, but the risk of getting immobilized too. The same dungeon also features Hammer Bros (which generally appear along Gunner Guys, for extra fun). Hard-to-dodge and very powerful attacks make them one of the most dangerous enemies in the game.
Game-Breaker: The Mush Badge, which increases the Brothers' power depending on how many mushrooms they have. Go ahead and buy 99 of each mushroom. No one will stop you. This also makes Great Force more usable. Great Force doubles the damage you deal while also doubling the damage you take; that second part doesn't matter so much because, with both Great Force and the Mush Badge, you can destroy almost every boss in one round.
Get Great Force ASAP, which is after Chucklehuck Woods. Have one Brother equip that and have one equip the Bonus Ring, which you must have if you have Great Force. If you fight every enemy in the game after and take little damage, you can one hit kill almost any enemy in the game. Bosses can get taken down in two turns. With the Bonus Ring, which doubles Experience if you don't get hit, Great Force's side effect of the Bros. taking double damage starts meaning less, especially with bosses, which have Save Albums right before them... needless to say, a Great Force-Bonus Ring combo destroys anything, enough to the point where it's plausible to take out late-game bosses without Bros. Attacks, including the final boss. Not as game breaking as the above example, but still makes the game pathetically easy.
The matching pants that complete the ensemble—the ones that boost your Stache stat (chance to crit for extra damage) based on your Mushroom count.
Utilize Chopper Bros. extensively at level 3, and focus your level up bonuses on BP, ATK and SP, and you have a boss-killer attack, even if you don't use the advance version of the move.
Get the Advanced Thunder Bros. If you get it right, then it reduces the enemy's attack so that they only do 1 damage with each hit. And, it works on most bosses! It only hits one enemy, but since many of the bosses have only one section, that frequently doesn't matter.
The easiest way to max out all of your stats is to drink nothing but Teeheespressos. This is because Woo Beans and Hee Beans are the only two beans that are both infinite and easy to collect, regardless of the fact that you can't specifically choose which stat you want to raise with Teeheespressos.
Troopeas, Elite Troopeas, Paratroopeas and Scaratroopeas. Why? Not only do they have very high defense, they can also heal or even resurrect other enemies in battle, including themselves, making them extremely annoying if you can't defeat them in one or two hits.
Magikoopas, for the very same reason as Troopeas (healing enemies and hard to kill), but with the extra feature that they can also boost other enemies or themselves, and attack with very powerful fire spells.
Malibuts. While they're not very strong, they retaliate as soon as you attack them, even if it's not their turn, and their attack have a fairly long animation, making countering them annoying and time-consuming.
Good Bad Bugs: Strength and Defense Buffs (and Debuffs) become permanent once you die. And they still stack with temporary buffs/debuffs.
Remember the entry about the Mushroom vs. Beanbean exchange rate? Now consider that Mario & Luigi: Dream Team ends with the Zeekeeper showering 80 million coins on Pi'illo Island, which would be used as a tourist attraction. Guess the big bird didn't really take inflation into account.
The penultimate battle against Fawful is a Shielded Core Boss. The final battle in Bowser's Inside Story is also a Shielded Core Boss, taken Up to Eleven. The Bros. have to attack the Dark Core above Dark Fawful's head, which they can't reach unless they take out his limbs, which they can't attack unless they take out his eyes. They can't even fight Dark Fawful at all until Bowser inhales him after making Dark Bowser spit him out.
In the intro, it is shown that Cackletta had replaced Princess Peach's (or rather Birdo's) voice with explosive vocabulary. Now even her words are bombs!
Ho Yay: Luigi is flattered by Prince Peasley. Also Birdo toward Popple, depending on what gender Birdo you think is.
It's the Same, So It Sucks: Aside from Minion Quest a majority of the remake's content is exactly the same as in the original, so if you played the original not much will be new.
Joke's End's music. Yes, there's background music that can turn into this because of how repetitive is. It's also the temple music from before.
"OH! Help me!"
The dreaded Hanna-Barbera "zing-out" whistle that plays whenever someone runs away during a comical moment. You're gonna be hearing that a lot throughout the whole game, mostly once during any cutscene.
In Bowser's Minions, the Bros. saying "Let's-a go!" every time they initiate a Bros. Attack can get very irritating after a while.
Many of the places that Cackletta involves herself with? Yeah, they become this. The Mario Bros.' first visit to the Beanbean Castle Town. The houses and buildings are all wrecked and innocent civilians lie on the ground like they're on the verge of death. The music makes it feel like you're walking in a graveyard. It gets worse, as you end the game with the town in this state. Yeah, after having a nice town for a good portion of the game, it's reduced to this sorry state by Bowletta during the endgame.
The Oho Jees. In particular, the research team that was studying them accidentally lit one on fire. End result? It attacked one of the scientists, and the scientist transformed into an Oho Jee. Oh, and the research team regards it as no big loss, saying that science marches on.
One-Scene Wonder: The very popular Geno makes a brief appearance as the host of a minigame in Little Fungitown. Some of his more dedicated fans have admitted to buying Superstar Saga once they heard of his brief appearance here. Unfortunately, his cameo is removed from the 3DS remake, likely due to Nintendo not wanting to pay royalties to Square Enix again.
Seinfeld Is Unfunny: Now that the main Super Mario Bros. platformers make a point of having Luigi playable and prominent, the jokes about his second-fiddle status and him staying behind to "protect the homefront" can lose some of the impact they originally had in 2003.
That One Boss: Some bosses in the game can be rather frustrating.
Trunkle can be a real pain depending on how you choose to fight him. The worst part about the mutant Sudowoodo thing is that there's no indication that you have to (let alone the fact that it's even possible) attack the orange in his hair instead of the beast itself.
Whichever friend of Jojora that you pick, it'll end up as this trope. If nothing else for taking too long. Especially if she uses her kissing attack to eat HP from your face or you try attacking her whenever Jojora is on the battlefield.
While Cackletta's Spirit isn't quite one, the beginning of the battle is. Both Mario and Luigi have only one hit point, and she gets to go first, unleashing a barrage of attacks that the player knows nothing about. And losing—that is, getting hit even once—means you have to fight Bowlettaall over again. The remake, thankfully, removes that part of the fight, letting you heal right away.
Ludwig Von Koopa in the remake. In the original game, he's fought very similarly to Iggy Koopa, but his fight is significantly changed in the remake. He charges up a giant orb and fires out smaller orbs, all which can be relatively tough to dodge. The smaller orbs deal a crapton of damage and the giant orb is instant death. Also, the battle is similar in the vein of Shrowser from the second game and Thunder Sass from the fourth game, where the entire battle must be won by counterattacking, nothing else. At least the game lets you start over right at the start of the battle.
Walking along the Seabed can be a pain due to the slow movement speed and awkward swimming controls. Special mention must go to the sections where you have to swim over a bunch of spikes. Thankfully averted in the remake, where you can swim really high. Still kinda awkward when swimming above objects that you'd technically be able to swim over normally, but can't.
Joke's End is a large and labyrinthine dungeon that contains extended sequences where each Bro has to explore alone through enemy-filled territory. The final dungeon is actually easier to navigate because it's far more straightforward.
That One Sidequest: At the beginning of the solo sequence in Joke's End, you can see an out of reach switch on Luigi's side of the fence that you need a barrel to reach. After the solo sequence ends, you won't find another barrel until right before the boss. You have to get Luigi into that barrel and slowly backtrack through almost the entire level so Mario can get on the barrel and hit the switch. As a result of the barrel mechanics, getting into any battle will result in the barrel breaking and having to go back to where the barrel was. The reward is only Hoo Beans, of which the game practically gives you 15 of after finishing Joke's End and can be farmed in the surfing minigame; thus, barely anyone does this once they find out. This is only the case in the original, however; the remake, where it is required to get all of the blocks and music, makes it much easier to pull off. Funny enough, the original barrel still appears in the boss room, despite now being obsolete.
Fans weren't happy that some of the original GBA version's more cartoony animation and effects were downplayed in the 3DS remake (for example, the Toads no longer get Blank White Eyes when Cackletta and Fawful steal Princess Peach's voice at the beginning of the game, and when the Mario Bros. and Bowser meet her afterwards, her tears are no longer Ocular Gushers, but instead exist as mere particles that don't even hit the ground).
Some fans are also annoyed the remake changed some of the more unique character designs, such as the Koopa Troop members getting the standard Koopa design instead of the GBA version's helmeted design. The redone graphics have also gotten complaints in some circles, particularly the mountainous areas.
The music has also been the subject of derisive comments. A particular example would be the rendition of the final boss music, where the organ music seems to overpower the electric guitar.
They Wasted a Perfectly Good Plot: The Beanstar ultimately plays no role in the story besides needing to be recovered and then reassembled, which is really a shame because this is a highly sought-after wish-granting trinket we're talking about here. Heck, you never even see it awake outside of its backstory and for a few seconds during the credits, which has led many to wonder what its personality was like (if it had one; it does seem sentient). This is especially glaring during the endgame: since Peach had been rescued by then, she could've woken it up so the Bros. could wish for a way to access Bowser's Castle in the sky, but they get there with Blablanadon instead.
What an Idiot: After Mario and Luigi put the Beanstar back together, they get a message from Bowletta, where they want Mario and Luigi to hand the Beanstar over to them at Joke's End in exchange for Princess Peach's freedom. After the message is done, Prince Peasley proposes to use a fake replica of the Beanstar to give to the baddies to trick them without giving up the real deal. Unfortunately, Fawful sees through the trick and knocks out Luigi when he shows the fake Beanstar, and steals the real one from him. The question here is, why bring the real Beanstar in the first place?