Is Pinyin recommended for Mandarin Chinese?
Hanyu pinyin (or pinyin) is the de facto standard for transliteration of Standard Chinese, especially for materials using simplified Chinese characters. In the last ten years, I have used or browsed textbooks, dictionaries and other learning materials; some of them were entirely in Chinese, others were for native speakers of English, German, French or Dutch. All of them used pinyin as their transliteration system. 

I have also met learners who found pinyin non-intuitive, especially for the sounds represented by q, x, j and c. I have known people who devised their own transliteration system but abandoned it some time later.

If you don't want to use pinyin, you will have a hard time finding learning materials for simplified Chinese characters that use a different system; these materials are available but are typically at least thirty years old.