^ Tim Burton and Jon Favreau had comedic backgrounds before making Batman and Iron Man respectively.
I really doubt that, having so shrewdly guarded their movies and adhered to a winning formula and consistent tone to date, Marvel will suddenly allow Captain America 2 to become a Batman and Robin type jokefest. Any more than Iron Man 3 will turn into a Lethal Weapon clone because of Shane Black's involvement.
Marvel have been quite bold for the most part in their choices of directors (Whedon and Branagh especially) with only Louis Leterrier perhaps being an uninspired choice (IMHO). If they saw something in these guys, I'm happy to go along with them, even if I wish Johnston was returning.