sk - sure, one of our Big Projects for next year (as part of the larger-scale flashcard system redesign) is allowing for more sophisticated formatting in user dictionaries and custom flashcards. Though a big thing we'd debating now is whether to give users more control over formatting (bold / indent / etc however you like) or whether to keep fine-grained format control a Pleco-only thing and simply let users tag content semantically - you specify where the examples / usage notes / parts of speech / etc are and we figure out how to render them prettily (and then update that format as it changes in our app).
"browsing dictionaries: in popup mode the menu bar is positioned too high" - could you expand on this? Not quite sure what you mean by "browsing dictionaries" (which exact screen?) or "menu bar" (the top toolbar?).
Saving clipboards (or any type of file) directly to Dropbox proved problematic so we punted that for now but will bring it back in a few releases once we've gotten the bugs worked out - not supporting it seems better than supporting it and having files go randomly missing / not save correctly.
For flashcards, in Settings / Flashcards you can configure the list layout in flashcards to be whatever you like, so perhaps it would make sense to separate the headword / pinyin / definition more.
sych - old issue, actually; difficult for us to fix directly since it's happening at the lower levels of our OCR library, but we've been slowly replacing a larger and larger portion of its code with our own and eventually should be doing pretty much all of the front-end processing (figuring out where lines of text are) ourselves, at which point we can make more headway on this sort of issue.
Alexis - good catch, thanks. But which toolbar are you referring to? There isn't any toolbar on the bottom of the screen in 3.0, except for the optional dictionary-switching slider and that should move itself above the keyboard when it's open.