Change settings to proper twoside with important bits on right (like a book)
Improve microtype settings
Ragged2e breaks alignment of stuff in captions
Capitalize all Equation/Figure etc and don't use abbreviations
Make the references numerical, unsorted, provide backreferences to click, show all names, use iso dates
Make all figures default to 75% textwidth
Reformat file inclusion rather than input, show example of appendix
Fix up header/footer
Clean up frontmatter, provide citation example