What are TeX's limitations in typography, book design and publishing? (and here TeX also includes all its derivatives, like pdfTeX, LuaTeX, and macro packages built upon it, LaTeX, ConTeXt etc.).
Some things (like math and references) are extremely easy in TeX. There are some things that are harder to do in TeX-based systems, but they are possible, even if cumbersome (like precise control of images' placement or manual control over layout and design). Solutions to some problems have been found (like
microtype). Some things are rarely talked about (like color profiles).
Please mention what is either extremely hard to achieve with TeX or is not possible at all (due to inherent limitations of TeX, or due to bugs/limitations in the available tool chain). Please mention also which technological steps do not fit well with TeX workflow.