I recommend latex, as once you get going it is not really all that complex, what with all the packages available.
You can, of course, write natively in LaTex but the program wasn't designed for that.
Hard to know precisely what you mean by this, but if you mean that you shouldn't be writing things like
\documentclass{article}
\begin{document}
Hello world.
\end{document}
then you are mistaken; the LaTeX book (and many other documents) describes what to do. If what you mean is that a person is somehow meant to use a front end such as LyX, then you'll get a lot of disagreement (such as from me).