[capnrefsmmat]

I'm a big LaTeX fan, but the core typesetting engine is pretty heavily focused on print layout, so you'd have to restrict your macro subset to produce clean XML reliably. (You'd also have to see if you can produce JATS, the standard XML dialect for journal articles.)

I don't know of any good alternatives. LaTeX succeeded because of its excellent extensibility, so the core can be used to produce almost anything. I'd like to find similarly extensible tools that can cleanly produce XML as well as PDF. Maybe Pollen (http://docs.racket-lang.org/pollen/) will be one.

There's also Scholarly Markdown (http://scholarlymarkdown.com/), but I suspect Markdown's lack of easy extensibility will doom it, since you'd have to write documents that fit narrowly into the features they provide. (What if you want a "remark" environment and they don't provide it?) reStructuredText is also an option, since it's built for extension, but it's not very well-known outside of Python circles.