Don't backup Downloads, keep a reference file instead
I like this idea a lot. Don’t backup the Download folder, but keep a text file with the contents, so that it’s easier to redownload all the stuff. I’d say one should automate this task with Hazel or Keyboard Maestro.
Let’s say to run once an hour:
ls -R ~/Downloads > "$HOME/Documents/Downloads History/$(date "+%Y-%m-%d %H-%M") Downloads.txt"
This way you could have a history of your downloads in the Documents folder with a date added. Thus Time Machine would backup the file and you’d have an easy overview of the last status.
Of course one could run this less often than once an hour.