Bear in mind the software of the Kobo is very limited compared to the Onyx. If you don't like what you can do with the Kobo (including Koreader), you're stuck. If you don't like what the Onyx does, you can just install another app.
There is also a program on here that you can use to pre-process pdfs and change their size for your screen. I can't remember the name of it. Anyone?
Edit: here it is.
http://www.willus.com/k2pdfopt/