1. Language: Typically, you go to a different world where a different language is spoken, but for some reason they have the same grammatical rules as your original language, or at least that's the most logical conclusion you can think of.
In most Japanese stories the protagonist still uses "honorifics" or the "formal way of speaking" and it seems that no one in that world; I repeat, he uses a different language, it seems strange to him that someone adds letters to the end of his name or sentence. Moreover, the same natives seem to follow the same customs of the language. The only way I see this being halfway justified is if they have an ability called "translation" or something similar. But in many cases the protagonist learns the language from scratch so it really is strange.
Unless you want language barrier to be a key point of your story, then you should not, on any occasion, introduce more than one language.
I mean, sure, you can simply handwave the language problems away with translation magic, but that basically amounts to the same end result of having a single language.
Fact is, you want your characters to be able to properly communicate, and your readers to properly understand what is happening... So, if someone is isekai'd to a different world, and they magically happen to talk English... Then you were just lucky that English exists in a different world. That's all there is to it, and that's how you should write your own novels too. Everyone in the entire world should speak English and nobody should ever question it... Unless you actually want language barrier to be a key point of your story, of course.
2. Only Japanese?: In several stories where there are several individuals who go to other worlds or in the story you mention that there were more people as the protagonist, for some reason they are all Japanese. Until now I have not heard of another nationality in these kinds of stories.
Very similar to the one above. No point in multiple isekais taking people from different cultures, as it will just make it harder for your readers to relate to the characters. Especially if your target audience mostly consists of people from your home country.
Just think of it as a lucky coincidence. No need to overthink it too much. It's easier on the readers and on the author if it's done like that.
3. Food: The Japanese seem to love their food to the point of having to replicate it in a different world, but it's just too unnatural for all of Earth's plants to come into existence in the other world, after all so many of them have been created Through artificial selection, even if the same plant were to exist it would probably be a degraded or primitive version of it.
It is also quite strange that the natives find it the most delicious food they have ever eaten.
According to my own research on the best restaurants and best cuisines, Japan is not among the first.
You don't have any need to invent new animals/plants when writing a story in a fantasy setting. The reader will more easily relate to apples than to Grewhala, the round red sweet fruit.
Sure, if your novel is cooking-focused, you can introduce new unique magical materials to work with, but... Otherwise, sticking to the things that already exist IRL is simpler and more efficient. No need to introduce new plants/animals to your reader if it's not relevant to your story. You're just putting an unnecessary burden on their memories, since, differently from you, your readers won't keep a well-organized glossary that mentions all terms that you introduced to the story.
As for the thingy about the native people loving Japanese Cuisine... This one I will agree that is a bit of a stretch, but it's fine if they happen to not have had very tasty food to eat in general. If most of what they ate consisted of simple grains, they'll probably be very much in love with any kind meat and/or sweet.
4. Medieval or modern: For some strange reason you find yourself in a different world that seems to be set in the middle ages, but for some reason they look clean, they wear decent clothes, the place does not stink and they have objects that do the same functions as the that we use in the contemporary age. The reality is that in the middle ages commoners looked like homeless people, the streets are full of excrement from both people and animals, the houses are made of wood, the floor is dirt, no urban planning and of course let's not forget of the medicine made of mixing things at random or the lack of hygienic care of people.
Believe me when I tell you that a tramp today has better living conditions than a commoner in the middle ages.
While yes, commoners nowadays do have a better living standard than nobility did have in the middle ages, that doesn't suddenly make historically inaccurate depictions of Medieval people truthful.
@Agentt already wrote plenty about this point, so I won't go too much in-depth... But I will tell you to try doing some research before assuming that "common knowledge" about medieval settings is true. Otherwise you'll start thinking that water was too unclean in medieval times, so people mostly drank beer instead (Yes, some people think this is true. Crazy, right?). Like... Seriously, why do you think wells exist? To get water... Clean water (not to mention tons of clean rivers existed too, and people actually used those).
5. Inventory: There is always the typical storage or inventory ability that only allows you to put non-living things inside and also freezes time.
The reality is that the function of stopping time is unnecessary, after all the decomposition arises from fungi or microorganisms that travel through the air, if the ability does not allow living beings to enter then they will not be able to decompose them. Although there are some that break down by chemical reactions, but they are not really abundant. The same is for objects that are eroded by air or water, if the ability only lets in the specified object then it will remain intact. This is what is normally known as void sealing, the thing is that the ability is an absolute void.
This is a simple plot-device for convenience's sake. I don't have much to say about it.
Sure, the time-stop is unnecessary, but it doesn't really harm the narrative in anyways, so it's fine.
And well, you totally can make a narrative without an item box... The item box just makes it more practical for authors that don't want to think too much about logistics.
Bathing being lecherous and prone to bouts of sexual frustration as per the rules of purity. While the common folk know they are covered in cow shit and might as well tell the system to go fuck itself and be clean. An addendum to this is that teeth cleaning was done with ash water and not solely reliant on being in contact with sweets.
This is mostly false tbh. Most people (nobility and clergy included) in Middle Ages did bathe regularly.
There were indeed a very very very small handful of people that almost never bathed (from the top of my head, I can recall one noble and one member of the clergy), and their actions were seeing as more of a martyrdom than a practice other people were expected to follow... And yes, people were aware of how unhealthy it was to not bathe.
Similarly, Medieval folks were also aware of what things were more likely to make teeth rot, and did regularly wash their teeth, so they didn't have nearly as bad of a dental health as you're portraying.
