I'm also interested in that, but like ikarus9999 I'm using C++ and Qt. Nickel already provides an interface for the development of custom plugins, so I think it's a good idea to base on the official software and just extend it where necessary instead of developing everything from scratch. Most things can be modified with some work. Writing a custom pdf reader (maybe based on okular, see
http://code.google.com/p/qindle/), a more advanced library view or some kind of wireless sync should be possible.
libnickel exports pretty much everything and in addition we have qt introspection, so it's possible to interact with almost the whole system.
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I'm also investigating the Touch and playing a little bit with C++ and Qt. I'm still having issues with the screen refresh and the input.
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If you don't get input events, try QWidget::setAttribute(Qt::WA_AcceptTouchEvents);. This did the trick for me. As for the screen refresh, I'm also having problems with that. At the moment I'm trying to extend the "START" menu on the homescreen with custom options (something like rescan the onboard storage for ebooks would be cool, since copying books via scp is trivial but nickel doesn't recognize them immediately). But even though I can get a pointer to the menu and add new entries/change old ones the menu itself as displayed doesn't change.
Edit: I also got qtscript to run (which was trivial), and this might be a great way to do minor customizations.