These don't fix all the problems mentioned, but they definitely fix this one "It is grossly non-interoperable with other modern scientific tools, and mainly it is unable to embed interactive (i.e. “non-dead”) content generated by other tools.".
But why prefer Latex to HTML? Latex makes a beautiful, well-structured document every time. I don't think I've ever made something beautiful in HTML.
Comments
A couple of alternatives you might enjoy:
http://www.stat.uni-muenchen.de/~leisch/Sweave/
http://orgmode.org/worg/org-contrib/babel/
These don't fix all the problems mentioned, but they definitely fix this one "It is grossly non-interoperable with other modern scientific tools, and mainly it is unable to embed interactive (i.e. “non-dead”) content generated by other tools.".
But why prefer Latex to HTML? Latex makes a beautiful, well-structured document every time. I don't think I've ever made something beautiful in HTML.