I am doing well enough recording facts, notes, media etc. in my Family Tree Maker software and I suspect all other major competitors are somewhat similar for just recording and organizing data. What I'm finding, though, is that none of these seems to have any kind of POWERFUL reporting or publishing capabilities. For example, The Complete Genealogy Reporter can take a GEDCOM and generate an entire book, with a multitude of settings for formatting. Ancestral Author does something similar but without charts. Neither of these is quite up to the standards I'm looking for. In addition, I'd like to do more analysis, such as forenames, regions, date spans, and ad hoc queries that would expose patterns I may have missed looking person-by-person in linear sorted reports. A matrix (spreadsheet) report showing family members down the left side with dates across the top (think census, birth, death, marriage and arrival) and the information in the cells of the matrix would quickly expose "holes" in family research for those people for whom I've not located census information, etc.
It seems like the free GEDCOM tools are severely lacking in this area as well, but I don't mind paying for good-quality software that's more powerful than what seems to be the most popular programs. Is anyone else trying to generate and publish a book without tagging every item in publishing software to enable generation of hyperlinks and TOC, index of people etc? Are any of you truly able to generate analysis reports that help you discover? If so, I'd love to hear what tools you are using.