User blog comment:Master Sima Yi/Assassinews 28-02-'13 — Assassin's Creed IV: Black Flag revealed/@comment-4829046-20130301065828/@comment-4928711-20130301122201

Maybe they called it Assassin's Creed IV: Black Flag because even though it has a new ancestor which is why they added in the number. Its setting and time period is very close to Assassin's Creed III which is why they added in the Black Flag.