Interesting article. You have obviously put some thought into this. Perhaps the endorsement to download ratio can be improved by providing better real time reminders (in the profile page or tracked files interface) of what the user has downloaded, to enable them to rate their downloads with a positive or neutral response, much like acknowledging when a message has been read. So that the downloaded files will get the same prominent location in the user profile page as messages and ability to hide a download rating notification will only be granted when the user has responded with positive or neutral rating.
I also suggest a better mod summary interface to allow users to see when a mod has been updated. It would be great to also have the ability to remove the lengthy articles from the tracked files stream on the front page and provide a view that only shows when the main file has been changed, for example.
Sometimes it takes me a while to endorse a mod, even to the point of Nexus forgetting I have downloaded the mod after a couple months. So I periodically go through my hundreds of mods in Wrye Bash and try to endorse all the ones I am still using and happy with.
Keep up the great work!