I'm looking into the LZMA SDK. If I can get it to work on the 3DS, all the formats you mentioned will be supported. If not, at the very least .cbz file support (via zlib) will be included at release.
There will also be support for custom themes, and I'm trying to implement a Manga/Comic Downloader similar to the one featured on the current Manga Reader. Not sure when a release will be ready, but my current progress is on GitHub. I could release the source if anyone is willing to compile and try it as it is now.