Originally Posted by st_albert
The biggest fault is that all the body of the book will be in a single .xhtml file within the epub, which will break some readers.
I know, because our small publishing house is now involved in converting our print books (imposed in InDesign) to epub, and I get the task of tweaking the output of ID4 so it will meet our standards.
If you're still using InDesign4, then you can fix this by restructuring your book in InDesign. Instead of laying out the book as a single document, create a 'Book' which contains each chapter as a separate document (you'll probably want to do the same for the cover, title page, front- and back-matter). Each separate document will then be output as a separate flow and this should solve the issue with flow-sizes. This is rather clumsy and involves pasting a lot of pages into new documents.
ID5 allows you to control flow breaks through use of heading styles which have been specified in the ID-generated Table of Contents. There's a video demonstrating the process here
If you use a lot of internal links in your book you'll want to take a look at this
blog post and use the script linked there.