As you don't tell us what your problems with the LaTeχ approach are, it's hard to give good advice on how to proceed.

Personally, I would look at producing the appropriate HTML files instead of LaTeχ if that is easier. Both are still simply text files.

I think that LaTeχ still has the best facilities to automatically generate a table of contents, list of figures etc., but you can always program these yourself. I am unaware of any "framework" or set of libraries that is geared towards report production which has readymade reporting features like you seem to want. I would also look at Crystal Reports or Microsoft Access - these are applications geared mainly towards report generation and they have far more ways of producing fancy charts.