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I don't know what problem you're referring to JCSullivan, but it seems you're more pissed about the nature of PDF's and not the Kobo itself.
PDF's were designed for publishing/printing purposes, and as such uses absolute positioning based on the page size... which makes in inherently unfriendly to 'reflow' concepts like font resizing. Essentially, PDF's are made to be 1:1 digital copies of print material.
So taking PDF's that are created with a standard page size, and viewing them on a smaller screen like the Kobo's is probably not ever going to be elegant. You're probably always going to be limited to simple zooming and panning.
The only way around this is creating the PDF's so the page size is as small as the Kobo screen. Since most of my master copies of my books are HTML (epub is just HTML/XML wrapped in a zip container), cooking a PDF with an appropriate page size is easy, and reading on the Kobo doesn't require panning around.
Of course, if your master copies are already PDF's, this won't be very helpful to you. Which is exactly the reason I try very hard to avoid PDF's as master copies for ebooks.
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