Japanese writing system is difficult, no one would disagree with that. There is a lot of aspects that make it difficult other than having a couple of thousand characters and various different readings for each one. I want to shed some light on another aspect here, Kanji as we know now has a long history before it was established in Japan, therefore there are many conventional usages to which people have accustomed over the years, and thus not easy to change; especially that their education support these conventions. But to Japanese learners it’s very confusing to learn all these conventions, naturally being able to adhere to it in writing becomes a very difficult task.
Japanese writing system is unique in that it has stringent rules and at the same time has some level of freedom, which when you master will find fascinating, however to struggling learners it represents a great challenge with many obstacles.
In the sentence 「動物園にライオンがいる」is sentence using all 3 types of characters (Hiragana, katakana and Kanji) and probably there is no other (proper) way to write it, 「おやつはプリンだ」is another sentence where everyone would agree on writing it this way. It is possible to write「おやつ」as「お八つ」using the Kanji number which it’s originates from, but in the real world no one writes it that way, so everyone would probably write 「おやつ」, also 「プリン」has no other way to write it.
It was mentioned in an article I read that an Italian student came to Japan to study Kanji, and one time her teacher asked for an essay titled「おやつはプリンよ」at that time she didn’t recognize the word プリンand she was wondering “what is that purin?”, but she thought it must be some Japanese snack, so she wrote it in Hiragana, and her teacher later corrected her saying that it should be in Katakana as it’s a loan word. To her surprise purin was that yellow sweet desert, and it wasn’t 「プディング」as most of us (foreigners) might expect. However, when Japanese people hear pudding they will most probably write it 「プリン」. Katakana words are usually different from the original words, thus make it difficult for foreigners living in japan to understand it.
So sentences like 「動物園にライオンがいる」「おやつはプリンだ」, except for elementary students who can’t yet write the Kanji in 動物園 more than 99% of Japanese people will use the correct usage of when to use what type of character. But Japanese is not that easy, but in the following example sentence 「隣の奥さんは別嬪でほんとに羨ましい」I don’t stalk people’s wives. It’s just an example, but young people probably don’t use the word 別嬪anymore and if written in Hiragana they will understand it. Also for ほんとにit can also be written 本当に, as well as うらやましいit can be written in Hiragana or Kanji. Different people will have different ways to write those kind of words. Another example is 「晩ご飯は、たけのこご飯とほうれん草のおひたしです」this is again one sentence that is possible to write in different ways according to different people. Many people criticize the lack of definite rules in such writings. But I don’t think it’s a bad thing. Recently you can see some people write the word 「携帯」in katakana 「ケータイ」among other words that can be written in different ways, this means that you can express different meanings or emotions when writing. There aren’t many languages that allow you to write the same words in 3 different ways. If you think out of the box you might see that it’s actually brilliant. One advice I can give you is
When you read Japanese pay attention to how words are written, and to how natives write in general, in other words try to pick up their writing conventions by astute observation.