Shikamaru surely has the wits but he might be lacking in the spirit and charisma departments. A hokage can have aides to help in making wise decisions but if he's not motivating people personally or doesn't want to do his job, it's a problem. We already see Tsunade has some problems with the fact being a hokage basically means working 24/7, and as it is, Tsunade wouldn't have ever taken the job if she hadn't been under such circumstances as she was.

Shikamaru so far only has wanted to do what is absolutely necessary for the people of Konoha and otherwise just laze around doing little. And if you have a hokage like that, soon you will have a village full of lazy buggers concentrating on lounging rather than developing and running the place.