Nintendo shouldn't increase the licencing fees for their console, it would drive away third parties. But yes, it is true that in many ways, they are in a unique position because not only are they a console creator, but also a competitor for other companies on their own systems (and other systems) at the same time.
Still, as they found out with the N64 and GC and are finding out now with the Wii even in the #1 spot, they need third parties to make a successful console. But as third parties are finding now, they can't just ignore Nintendo anymore, because Nintendo can turn the tables and become nearly 60% of the entire gaming market themselves.