Ideally, SEO should always be handled by the theme. Actually, most plug-in behavior that impacts the front-end of a site should be handled by the theme. Plug-ins like All in One SEO are quick solutions for people who don’t want to invest the time required to re-code a theme they built, downloaded from a free site, or purchased from another developer.
Putting the functionality in the theme itself gives you more control, makes WordPress faster, and means you don’t need to worry about upgrades potentially breaking your site if they introduce new bugs that conflict with other systems you’re using.