Quick follow up, I found the excellent
Comparision of iOS e-book reader software thread, and decided to try the ones with annotation or highlighting support.
* The book doesn't seem to slow
Blio down at all, although the stress marks are
displayed under the letters, nearly hidden. Annotation and highlighting works perfectly, although iBooks's version is a bit more advanced.
*
Kobo appears to have more trouble than iBooks; while stress marks are displayed correctly, it
refuses to let me highlight or make a note; it pauses and then nothing happens.
I'm going to make a post on the Apple forums; The only problem iBooks has is the large amount of pausing. Stanza has no such speed issue, which makes me think that it has to do with how it's processed or something.
I may edit this post later to add in any more I test.. this is becoming something of a personal quest
Could the ePub itself be the problem? I didn't find anything much extra in the code, just paragraph tags and so on. Flightcrew only finds an XML dtd mismatch, which doesn't seem like it would bother a reader too much...