I use the term "retired" very loosely here, as I'm perfectly okay with the "old" protagonists making a comeback. A better way to put it would be, a new main character with a long-term position, and nothing short-term (like a couple of chapters).
Examples:
Tengen Toppa Gurren Lagann
Spoiler (mouse over to view)
Kamina seems to have a lot of exposure at the beginning, but then he dies, and Simon takes the lead role.
Dragon Ball (subverted)
The author had originally planned to replace Goku as the main character with Gohan during/after the Cell saga. He later changed his mind.
Genshiken
Spoiler (mouse over to view)
If we assume Sasahara is the main character, he has since graduated from college, and Ogiue seems to have taken his place.
20th Century Boys
Spoiler (mouse over to view)
Kenji disappears for a good chunk of the series and doesn't come back until towards the end, while a grown-up Kanna gains presence.
JoJo's Bizarre Adventure
The series is divided into parts and there is a different protagonist for each part.
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If I've made a thread in the "I'm Looking For..." forum, I am only interested in Japanese manga. I am not interested in non-Japanese media at this time.