Fonts are thickening in images of layouts

Illustrator is NOT a PDF editor, neither is Photoshp. If you want to outline Text, do it in Acrobat Pro. Transparency is not a problem in modern workflows, use PDF/X-4 to keep transparency and layers.

Don't outline fonts, and don't use transparency over areas with fonts. DON'T USE JPEG!! Don't rasterise. Given that, it should print just as well as the original, allowing for the scaling down. 

If that doesn't happen, can you please share a sample PDF we can check out?

Have you tried placing PDF without outlining or rasterizing the fonts?

That sounds like a very questionable workflow to me. What does "images of InDesign layouts" mean? Why are you opening PDFs in Illustrator? Unless they were created by Illustrator, you will destroy the integrity of the layout.

Finally, if you want us to really understand the issue, screenshots at a minimum would help and the files would be even better.

I have images of InDesign layouts I am putting in InDesign brochure.

Did you try to import the native InDesign files in your brochure?

Some possibiles:

1. When you change your fonts to outline, you lose all hinting that improves printing at smaller size. Outlined fonts will always look "fatter" than live type.

2. In the same vein, rasterized type will also look different

3. Your type may be interacting with transparent areas, and depending on how your are exporting these, may be rasterized/flattened whether you want them to or not. Sometimes  reordering layers to keep type "above" all possibly-flattened areas helps

Depends on your file!!

Hard to know exactly without seeing some screen shots/sample pdfs