As I understand it the problem with embedded fonts is not entirely universal, some books with embedded fonts do work and some do not.
When it comes to books purchased from Kobo and loaded in Kobo format (only through the Kobo/Borders/etc app, not through Calibre or copied to the Kobo manually) these do not contain embedded fonts? The original Kobo's format doesn't support the embedded fonts, the new format (released on the current Kobo WiFi and the Kobo apps for iDevices) they may be supported but I'm not sure.
When it comes to ePub formatted books then again "it depends", unfortunately. The ebook publishers have different approaches they could use to format their ebooks, by one method the embedded fonts do not work, if done a different way they do work.
At this point it seems if your primary concerns with an eReader purchase are eBooks with embedded fonts, newspapers, "book collections" or a lot of display options (more fonts, sizes, adjustable margins, etc) then you ought to look at other devices on the market. If you want a fairly basic, low-cost and relatively nicely integrated ebook ecosystem (dedicated eReader device, online bookstore and smartphone+tablet software) then the Kobo is well worth investigating.
Mind you I have not tried embedded fonts so I may be wrong, I'm sure others may be able to shed more light on the situation, my information is what I have picked up second hand by reading the forums here.