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Not sure what the current status of this problem is but here is some food for thought.

1) Even Adobe doesn't properly embed fonts in a PDF when doing a direct to PDF export from their applications. You would need to run a diagnostic on the PDF to ensure that the glyphs match up with the glyph table. Many times they do not if multiple PDF's are combined into one new PDF. But going the "old way" of making PostScript first and then making a PDF is not without its problems. Especially if you are trying to make an "ebook" like these. Also never use "use local fonts" in Acrobat when viewing a PDF.

2) Adobe applications properly honor color management settings. For greatest compatibility all RGB objects should be converted to and tagged as sRGB.

3) Even though PDF is an ISO standard it is not necessarily implemented in a standard way. And that's just making the PDF itself. We haven't even begun to talk about rendering a PDF on screen...

4) Windows and Apple operating systems are inherently color managed. Linux is inherently NOT color managed. Your monitors are not color managed. So anything you see that is "too dark" or "too light" is most likely attributed to that. How to solve it? Get color managed. But that's not realistic. It's not a simple problem to solve. I guess it could just be displayed "wrong" by not using color management.