Adobe Indesign is wonderful for publication design (meaning books, newpapers, flyers, magazine, etc). As a graphic designer, I use it when creating process books for my projects, presentation books for the final results of projects, and animated EPUBs (meaning an animated book).
If you were to try to create a bunch of pages in Illustrator, the file could become too large causing your software to function slowly. With Indesign, it can function well when multiple pages are present. Grid systems (meaning the system you have for your visual layout) are important in publication design, and Indesign functions more efficiently for creating/managing grid systems in a publication. InDesign can also easily take in files from Illustrator and Photoshop.
If you are looking for a more intuitive process, start with a layout plan on paper and then digitalize those ideas in InDesign. Hopefully this answer helps with your question.