If I'm writing a paper, I use LaTeX. Yes, the macros are a pain, but I find it takes less time than writing a paper in, say, Word (page breaks, sections, image placement, etc. need only be written once in LaTeX, but in Word they need to be revisited at each draft); and LaTeX's output quality meets my standards (while Word's, say, doesn't).
If I'm writing documentation, I use Markdown. It's simple and it has links. The output quality is far lower, because I expect readers to prefer reading plain HTML anyway -- a PDF would be inconvenient for them, even if it would be prettier.
Generalizing those notions:
1. The best tool for the job is the one that lets you produce and edit content as quickly as possible, while meeting your requirements. In other words: if monospace, left-justified text files are satisfactory, you should probably be using plaintext. When starting a document, first pick a set of features, then choose the tool that has those features and gives you the fastest workflow.
2. Distributing in multiple formats shouldn't be a concern: you can convert pretty much any open format to any other. Your _master_ copy needs to encode all the features you use.