OK, I’m not going to give a comprehensive list of what’s missing in the various incarnations of Bible software currently available, but there’s one feature I’d like to see which does not currently exist in any Bible software that I’m aware of — the ability to customise the morphological (and, when/where available, syntactical) tagging of texts.
Better still would be the ability to create multiple taggings for individual units. Then, in instances where the morphology of a word (for example) is ambiguous, that word could have multiple tags so that it gets caught in searches for either possibility.
I think that this becomes more important as Bible software moves into the realm of syntactical tagging, largely because syntactical analysis of texts can often be open to some degree of debate and so the ability to change clause boundaries, vary clause and phrase functions, and so forth, would be very useful.
For example, I’d like to be able to right-click on any item and have an option to edit the tagging. Select a ה and change it from the definite article to an interrogative ה, or if it is ambiguous, tag it both ways so that it appears in searches for either usage.