The generation of Table of Contents in FrameMaker has always puzzled me and in FM9 the Adobe developers have not made it any better.
Only being able to generate a separate file is the main design flaw. This limits your options as an author, whereas the approach of using some kind of Field for generated lists inside a file still leaves the option open to place that field in a separate file. As much as I dislike MS Word, this is one thing they did design fairly OK. Fields can be inserted almost anywhere in the document and each field has its own set of attributes that determine the scope, content and formatting. You can have multiple fields in the same document, no problem.
Not so in FM. You HAVE to use the separate file if you want anything that is automatically generated and updated. The very unhelpful remarks in the help files tell you that a) you can create a Text Inset from the generated TOC to place the TOC inside a file, or b) you can create a TOC manually using cross-references. Neither of those options should have been written down without making the help author die of shame.
And now, things have gotten even worse.
In long books you really want to embed a detailed TOC in a chapter and have a less detailed TOC at the beginning of the book. With the new option in FM9 to have books nested in higher-level books, this problem with TOCs could have been easily solved: create a subbook for each chapter, with a TOC in that subbook, and then have another TOC generated in the higher-level book.
The problem with this is that TOCs in subbooks are NOT included when printing the higher-level book. Whoever got that crazy idea ? Why would I want to include an entire subbook in a higher-level book if I do not want to include all of that book ? The only way around this seems to be to create an extra file in the subbook that uses a Text Inset to contain the automatically generated TOC. That file acts as a normal chapter in the subbook and will get included in the higher-level book. Of course it screws up the chapter numbering in the subbook, which you then have to manually correct. But if I then want to print only the subbook, I get TWO TOCs one after the other.
Did anyone at Adobe ever read anything about single-sourcing and reusing finished stuff (such as subbooks) in other publications (such as higher-level books) ?!
So, my request for a feature in the next release: get rid of the stupid method of generated files for TOC and other lists (a method that was probably designed when Fields still had to be invented in general) and stop defining how FrameMaker books should be structured. That is something authors should be doing, not tool developers.
For the current FM9 release, you should consider the exlusion of TOCs from the printouts of the higher-level books as a BUG. Fix it asap, please.