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.
YMMV: Ganbare Goemon
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Awesome Music: The soundtrack of Neo Momoyama Bakufu no Odori/Mystical Ninja is overall very good, given its use of Variable Mix. But the track from the final part of Gorgeous Music Castle takes the cake. It sounds like "Electric Eye" - and when you're comparing something to Judas Priest, you know it's So Cool It's Awesome.
Demonic Spiders: The masked carpenters in Ryukyu castle and the town preceding it in Legend of the Mystical Ninja that throw hammers that home in on the player. The hammers can't be destroyed, and they don't disappear after they hit the player, meaning they can easily hit multiple times and ravage your life meter.
Goddamned Bats: The lantern and coin-throwing enemies in Legend of the Mystical Ninja that appear in towns. The former's projectile can be knocked aside, but it's surprisingly hard to do so, and the latter moves much faster, jumps before attacking (meaning you have to jump to hit him as well,) and hurls a whole bunch of projectiles downward, meaning you're screwed if you're below him. It doesn't help that later levels are utterly clogged with them, to the point that grinding for money in town can actually be harder than the dungeon that comes after it.
There's also pickpockets who move faster if you're aligned horizontally with them, jump over obstacles, and steal your money if they collide with you.
The deer. They hurt you just like any other enemy, but you get penalized $100 if you attack them like with the bonus NPCs. They're even included in a really assholish trap where, if you visit a certain fortune teller and fork over $100 to get your fortune told, he simply tells you that he sees bad things in your future. After you walk outside, you're suddenly surrounded by deer, and either have to take a hit or lose another $100 getting out.
Replacement Scrappy: Shin Sedai Shuumei! and New Age Shutsudō weren't really bad games, per se - they just annoyed a lot of fans by thrusting an entirely new cast into the spotlight with nary a hint as to what became of the old favorites.
Sequel Displacement: The Ganbare Goemon series originally began with a Japan-only arcade game called Mr. Goemon, from which the original Famicom game Ganbare Goemon was loosely based on as well. Some gamers even assume that the first SNES game in the series, the one that came out in America as Legend of the Mystical Ninja, was actually the first game in the series, period. It doesn't help that the Goemon sequels for the Super Famicom in Japan are numbered in a way that they ignore the early Famicom games.
That One Level: Castle Ryukyu in Legend of the Mystical Ninja. The town itself is aggravating enough, mostly populated with projectile throwing enemies, but you can't even get into the final dungeon without shilling out almost $1000 on a phrasebook, meaning that unless you have that much money to throw around, you'll be spending even more time in town than you'll need to be. And then you get to the level itself and find a section where you have to fight the same hammer-throwing carpenters from before, only located in places where you either have to hit them with bombs or jump and pray that they don't hit you with a hammer and cause you to fall into a Bottomless Pit before you can get down to their level and hit them. And then after that is a series of very quickly moving platforms over more Bottomless Pits. The final level that comes after it is actually easier in comparison despite being a constant assault of Goddamned Bats, because at least there's no Bottomless Pits around and you can actually hit your enemies without jumping through hoops.
Best Known for the Fanservice: Yae's main purpose in the manga was to demonstrate that "sex sells," which definitely helped her become the series' second-most popular character.
Purity Sue: The manga version of Yae is one, which comes as a shock to those who were more accustomed to her no-nonsense personality from the games and anime. The only people who openly dislike her are Omitsu and later Ebisumaru, because they're jealous of her.
Toy Ship: Tsukasa Ishikawa and Asuka Tsuchiya in Anime.
Villain Decay: In the second OVA, Seppukumaru - who was originally strong enough to stand against Impact on his own - faces a humiliating defeat at the hands of a group of ordinary children.
Die for Our Ship: Omitsu is the favored punching bag for bitter shippers, as she is the sole love interest of the main series - a matter exacerbated by her lack of screen time outside of kidnapping plots, leading her to be denounced as a useless cuckoldress or simply ignored as a result. To rub more salt into the wound, Konami has been making Goemon and Omitsu's romance more overt in recent times, and even threw in a couple of moments to sink the more popular GoeYae couple. (The fans of the aforementioned couple have the manga and Bouken Jidai Katsugeki to go on, but they're Alternate Continuity so they "don't count.")
Unfortunate Implications: The series' tendency to peg foreigners as villains could come across as racist and xenophobic. This was subverted in the DS game, where the antagonist Peruri (obviously based on Commodore Matthew C. Perry) merely wanted to get some trades going with Japan, but was manipulated into evil by Touyama Kinemon, a native.
Taking into account the whole series is a outright parody of many of the cliches and tropes from the Feudal Japan era (something similar to Samurai Pizza Cats, except with more raunchier humor), this is understandable.
Unpopular Popular Character: Sasuke gets kicked around a lot, especially in the manga. Such is the price of being the most popular in the series.
Viewer Gender Confusion: The crossdressing Sister Bismaru is mistaken for a woman thanks to a typo in the Goemon's Great Adventure manual. There's also Sasuke, to a lesser extent.