How write an article when the "waterfall model" is not a good fit?
Whatever format you choose, you have to make sure that your audience can grasp what your paper is about within the first 4 sentences, that (s)he won't get "lost" while reading your article, and that it is easy to strategically skip much of the article and still get the main message. Remember that there is way too much being published, and that it is impossible to read it all. So most articles are only quickly glanced at and are only read if you convince the reader while (s)he is glancing at your article that it is interesting. This is the benefit of the standard format of articles. 

While writing your article, you are obviously convinced that your article is worth reading, but keep that reader in mind for whom your article is just one of way too many and who won't read your article very attentively. 

For example, the research process almost never follows the strick linear form in which it is presented in most articles. If that deviation is somehow relevant, then you can often use footnotes to discuss that without deviating from the standard form. For things that need more room, there are (web-)appendices.