Hey Jason,
There is always room for improvement, but currently we can't do much in that area. The thing is -> if you have hardcoded internal links it is extremely hard to change them to the correct url for your site.
The links in joomla depend on a lot of things - you can use sef or not, you can use a third party extension that creates them etc. You can have a link to a menu item, an article can be associated with multiple menus etc... That's why we are unable to offer a solution that can work right now.
My advise would be to watch the redirect component in joomla 2.5 -> it will show you the broken links on your site and you can create redirects for each broken link.
Kind regards,
Daniel
P.S. By the way have you used the parse function?
