An example of nuances? Many students tend to transliterate some common phrases that many teachers tend to let go like "fight!" for "gambatte". They can go unchecked for many lessons. If one of the students say that they have a japanese test tomorrow, another student will just say "fight!" and not be confused because they can both understand what was said and then move on to the next topic.
I would always correct students when they called Germany "Doitsu". Although that's much closer to how it sounds in German, it's not what we say in English, and common, non-traveling, English-speaking folk might not have any idea what they were talking about.
Well, children learn the plain (dictionary) forms first, and all other verb forms are built off of the plain forms, so it would make sense to teach those first. Also, it seems that Japanese people don't expect you to know the polite forms first.
I think the "problem" -- if you want to call it that -- is that most courses are trying to get you speaking like an adult as soon as possible. Probably because many textbooks assume you are learning Japanese for business purposes.
I agree that it would make sense to learn the plain forms first. On the other hand, many people never make it past beginning level Japanese so for those people it's probably good that they learned -masu forms. When they try out their limited Japanese they don't sound rude or like children.