Hey Thaya,
Such a great plugin you have here. Override the rel canonical instead of adding it automatically to the <head> is simply awesome. It 's been known as the downside of aio seo pack, which we don't really have any control of how to customize it for each page / post in any way.
Suggestions:There 're 2 for ya:
1. Admin Settings page.Though your plugin doesn't really need any settings in everything, in this page you could write some hints on how this plugin works, how to write the custom field, or any other faq stuff you have for this plugin, changes log, or even donation link.
Some users still think, when they 've activated this plugin - it 's done. As not many people really read faqs, a "Now What?" question, always poppin up. Or worst, some still thought, this plugin is their getaway for their plagiarism habbits. Lil bit writing from you in this page explaining something would help alot.
2. Custom field?It 's kinda cool if this plugin also write a form on each of new post / new page, just like aio seo pack did. While they 're really just write custom fields also - exactly like yours, they provide this form.
For ease of use purposes, that 's the overall idea.
All in all, you rock!