I'm not sure if I'll have an opinion that isn't commonly shared, so I figured I'd elucidate: I deeply love the simplicity of using markdown + LaTeX, however I realize that I'm somewhere on the gradient of complexity where I'm sacrificing some power for simplicity. Currently I think the tool that is used most is pandoc, and there are some offshoots that give pandoc more 'academic' power, like scholdoc.

I've just been hoping that the pandoc world would progress (add more scholarly features) so that I could continue to keep my own data locally, manage it in my own vcs, and process it with a makefile.

The only reason I see to hop on the software as a service bandwagon is for collaborative real-time editing (and some projects benefit greatly from this). I'll plug sharelatex for that, primarily because their model releases the software so that you can run your own if you don't want to pay for the service.