Do you get many issues that don't use your template because people go to /issues and click the new issue button? When I create an issue with a project, I typically don't a link in readme.md.
You could combine it with the new feature and put a warning message into the default box saying to click one of the links in the README in order to get an issue through.
It's not that the link isn't in the right place. It's that regular old users like me are familiar with the Issues -> New Issue workflow, and will continue to go right to that whenever we want to create an issue since it's a guaranteed way to create an issue.