Most people use Microsoft Word to write documents. And most scientific journals and conferences ask authors to submit their work using Word templates. In conferences, a Word template can be important to format the final edition of the proceedings. If you have different tools, you have to make sure the final result is the same which is difficult. With Journals, I guess the reason is that most people submitted their works in Word. But, with recent developments in writing software, is Word the best tool for writing scientific papers?
My experience has always been with Word because it was the tool most people used. And scientific papers are a collaborative creative process where all authors give their contribution, thus, we must use a tool where everyone can make adjustments to the paper. Otherwise, we print a copy, make adjustments on paper and someone else introduces them in the original file. Not practical. Word in not bad, but, from my experience, it’s not good enough. So, what’s the problem?
Most problems you experience with Word relate with formatting and indexing. Often we open a document in a different computer and everything is in the wrong place. Arghhh! Or when Word crashes, it could happen that some final changes were… just… gone! Arghhh! What I’ve noticed is people often loosing time on the formatting, and indexing (figures, equations, tables, references) – which is hard by the way-, instead of focusing on the content. And this is the main issue. When you write a scientific paper, you should solely focus on the content.
Well, we have other options.
LaTeX
Most of my scientific writing is made using an old tool. LaTeX. The layout is not appealing because it seems like you are programming code. And you are. But the outcome is always amazing, figures, tables, equations, references are always correctly indexed, and the design doesn’t depend on the computer you compile.
In fact, it doesn’t depend at all since you can use online platforms like 
ShareLaTeX.com or Overleaf.com to write your documents, including real-time collaborative writing with your co-authors. Something similar to Google Docs. In fact, this latter is the best tool for collaborative writing I’ve seen, and if your field doesn’t imply writing equations, or indexing figures, tables, it is a possibility, although it might be hard to format the document according to Journal’s requirements, implying you should export to Word to make adjustments before submitting.
Also, for offline writing you have free apps for all platforms like TeXMaker. A 
similar recent tool, and also free, is TeXstudio. For cross-macOS-iOS platforms, the best I know is Texpad, although only a free app for a trial period on iOS, it makes using LaTeX across devices easier and appealing. With LaTeX you’re less concern about the format and more focused on the content.
You still have some work with tables, sometimes with figures to put them in the right place, but the community of users is so vast you find almost every answer to your problems with a simple search.
In my experience, and after using online platforms with the ability for collaborative writing, LaTeX is the best option for writing scientific papers. The learning curve is slower, but once you become used to, you never go back… unless you could have WYSIWYG (What You See Is What You Get) and the LaTeX functionality for equations, figure placement, tables and so on.
Pages
With the new version of Apple’s Pages, we can now include equations using LaTeX, and the formatting when you change computer remains, contrary to what might happen in Word. However, indexing figures, tables and references is not evident, if it is possible at all. I confess I never tried. Therefore, it is an alternative with better formatting capabilities, but still limited.
Manuscripts
Now, this is a new tool. Recently, I began used it, and it seems to be a noteworthy attempt to provide WYSIWYG with LaTeX, and cross-reference with apps for citing references like Papers, and apparently you have templates for almost every scientific journal. There’s no version for tablets. Only for the macOS ecosystem. But, it seems promising.
My initial question stated “is there a best tool”. And in my experience, the best tool is always the one that works best for “you”. Also, any tool which promotes greater focus on content instead of loosing time with formatting is better. The challenge appears when you want to promote a more collaborative writing, which is now possible, but implies all co-authors to follow a certain platform and this is difficult. I think we’ll get there in the next few years.
QUESTION: What is the best tool for your scientific writing? Have you ever thought if’s this tool allows you to focus on content?