The problem with PDF is that they are meant for a given size and resolution, much like paper. The layout is fixed at the time of publishing. This works well for devices that can display at least that size, like a modern computer monitor, but not for 6 inch devices.
Reflow, various zooming options etc. are really only crutches for that problem. You want a text-based files, like .mobi or .epub. Or, get a full size reader like the Kindle DX, or one from the Pocketbook 9x series. I love my 360, but I don't ready PDFs on it (unless specifically formatted).
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