Going off a conversation in the Unpopular Smash Opinions thread, I think I'd make a Smash set for Dr. Cortex lean more into the pitiful, almost pathetic nature of the character, as that's what makes him stand out among gaming's trove of evil scientists. Give him a panicked rapid jab where he desperately flails his arms at the target, have his dash attack him tripping over and hitting people with his noggin, that sort of thing.
Of course he'd have his inventions, but you really need Cortex's personality to get involved to truly capture the character.