And then there are a bunch of nuances that don't follow logic. You just need to learn about them. For example, word "you" is always considered informal, a bit intimate and a bit rude in spoken Japanese, it can be used in formal written Japanese.
If you spoke English while only sticking to formal grammar rules, you'd be unable to communicate like a normal person at all.
I think the comment on the word 'you' sounding informal is a misunderstanding. People use a common formal noun for 'you', あなた, frequently; it's just the nature of Japanese emphasizes social relationships and makes it easy to drop references to people, so using such formal references can be stilted in the wrong context. But that's a matter of word choice, not grammar.
Even informal Japanese comes down to basic patterns for grammar.
>For example, word ...
Word choice is not grammar. Knowing how to use words correctly is the hard part.