What a horrible thing. Iwata will be sorely missed.
These days, few large company CEOs rise up through engineering (in this case, software engineering) to take the top spot at the firm. Iwata did exactly that, and that likely contributed a great deal to his success at leading Nintendo.
Nintendo needs a new rudder now. Who they choose to replace Iwata will make or break the company at this point — Nintendo is in a fragile position, poised at the edge of a transition to a new console business model designed to ensure its survival in a mobile/tablet/smartphone dominated world.
What will happen next is anybody's guess.
What happened under Iwata was amazing.