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I had similar problems since most of the (physics-related) articles I read have two columns of text and lots of equations and figures. I can recommend a free software tool called "k2pdfopt" written by William Menninger. It re-arranges the text flow of PDFs and optimizes them to the size of the e-reader screen. I'm really impressed by the results. Most importantly for me, it renders equations correctly and it automatically detects and reflows text in columns (even from scanned PDFs). It's not a perfect world, though, e.g. it sometimes misinterprets a hyphen that happens to appear at the end of a line for a dash, so when the positions of line breaks change due to text reflow then the two words that should be separated by a hyphen are merged into a single word.
You would run k2pdfopt on your computer and feed it with an article that you want to read. It outputs an optimized version of that article, which you can then transfer to your e-reader. As I use this tool a lot I wrote a browser extension that makes the conversion process a bit easier. It works with Chrome and Firefox and it adds a small button to your browser whenever you're navigating to the download page of a scientific article. If you click this button, the extension downloads the article, runs it through k2pdfopt, and optionally sends it to your e-reader. If you're interested, you may download the extension from my website (since I just know that some people are going to complain about alleged advertisement: please note that I'm not making any money with this browser extension and I'm just offering it to others because I find it useful and I don't see a point in keeping the program for myself. Also, I really think it's relevant to this question. So please, holster your weapons).
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