We're still going back and forth on that one, actually, in fact we may even make it the subject of a survey question. Basically, Pleco 2.0 supports two different dictionary database formats; one of them is faster, smaller, and non-editable, and that's the one we're using for all Pleco-released databases, and the other one (based on SQLite, just like the new flashard database) is slower, larger, but does allow entries to be edited, and that's the one we're using for dictionaries created by users on their PDAs.
The question is which of these formats to use for dictionaries created by users on desktops - smaller and faster but non-editable, or slower and larger but editable. We're leaning towards the latter, since these databases can be stored on memory cards (eliminating the size problem) and the speed should be more than acceptable on most systems. Plus, since it wouldn't be sharing the same format as our paid databases (like the current user dictionaries do), we could make the source code for MakePlecoDict 2.0 publicly available, allowing anyone else to create their own dictionary creator/manager utility.