If you want other output formats, there's little you can do to improve over pandoc. That will generate ePub, .mobi, DJVU, PDF, PS, and a multitude of other formats, on the fly. HTML is a valid input for most of those.

The main problem isn't pandoc, but HTML -- the crap that passes for Web-compatible today is simply any asshat's bad idea. I see as highly useful something which looks at what's been downloaded and reduces it to a hugely simplified structure -- Markdown will almost always be sufficient.

I've found, in writing my own strippers and manually re-writing HTML, that body content rarely amounts to more than paragraphs, italic/emphasis, and anchors/hrefs. Better-written content has internal structure via headers. Bold itself is almost never used within CMS systems for body text, it's almost always a tell for advertising or promotional content.

The sad truth is that manual rewrite or re-tagging of pages, in Markdown is often the best option I've got for getting to something remotely reasonable. The good news is that that's actually a good tool for reading an article, even if you find that on reading, it's not worth keeping :)