Best way is to save your .ai file with pdf compatible, that way if you edit the .ai file later the changes wil update in InDesign without having to create another file.
Cannot answer as to why your .pdf files are getting larger without knowing the contents. If you have a placed hi-res image in .ai, that would quckly give you larger file size.
Can we get a screenshot or some more information?
Wasn't there a way to save an AI file without the +100K of Color Profile data?
(Another big, big part is the "native AI data", but I'd have to check if that ends up in an ID generated PDF as well.)