Short URLs are still confusing. The best use I’ve seen is for people to attach a home-made short URL on the ends of their blog posts, so people can post using that. At a glance, you know which site it’s leading to and that it’s reputable.
Even then, I’m sure people still submit those links to shorteners like bit.ly and is.gd. My idea is as follows:
On your site, you’ll have a page which takes in a URL from your site and outputs a shortened URL using your sites URL shortener.
Shortening services could parse their URL to find the domain, send that domain’s URL shortener the link, get a shortened link back from that domain, then serve that. Or maybe that particular shortener would see if the length is above a threshold, determine that it’s too big, and just serve a regularly-shortened URL, instead.
Maybe it could find the path to the shortener by reading an entry from robots.txt, which we’d fill out with information. It’s worth a thought, at least.