SQL: subquery has too many columns

You are projecting three columns in your subquery, but comparing a single one of them in the IN clause. Select just the required column (r1.king) for the IN in the subquery:

SELECT kingdom.king, dinasty.birth, dinasty.death
FROM kingdom, dinasty
WHERE kingdom.king = dinasty.name AND kingdom.king NOT IN
(
    SELECT DISTINCT R1.king
    FROM
    (
        SELECT DISTINCT R1.king, D1.birth, D1.death
        FROM kingdom AS R1, dinasty AS D1, dinasty AS D2
        WHERE R1.king=D1.name
    ) AS R1, 
    (
        SELECT DISTINCT R1.king, D1.birth, D1.death
        FROM kingdom AS R1, dinasty AS D1, dinasty AS D2
        WHERE R1.king=D1.name
    ) AS R2
    WHERE R1.death-R1.birth < R2.death-R2.birth
);