Scimitar has a better critical threat range (18-20) instead of the 19-20 critical threat range of a longsword. If you're optimizing for better critical hits, like the Improved Critical feat and the Keen enchantment, that can become a pretty clear advantage.
Morningstar does bludgeoning AND piercing damage, and is 2 lbs lighter (and 4 gp less for a basic one, which might matter at character creation). Doing piercing damage helps when facing an enemy that might have X/piercing damage reduction, the lighter weight matters if the DM is strict about encumberance, and the lower cost matters at character creation when spending your starting gold.