Have you tried the research notes in FTM. I have not used it as it does not work for me.
I use spreadsheets a lot in my research. In fact I have one called Facts for each of my families. In those spreadsheets there may be a list of random facts that I do not want to lose but have no proof that it should be attached to a person in may database. Other worksheets maybe times lines, comparison of people suspected of being related, etc. Anything that may lead to a connection.
I also write extensive word processor documents, with detailed descriptions of specific research results and conclusion. I include section of the documents where the information I am using, is contained.
I don't think there is any genealogy program that will have all be able to replace spreadsheets and word processors for the way I am using them.