When you read several of the comments Nintendo makes about secrets left with the Nintendo Revolution (and even going back to previous systems) you realize that Nintendo views secrets as anything about a system they are not telling us about yet.
The most recent IGN interview is a great example.
paraphrase:
We have several little secrets we have not talked about. They could be games, or hardware, or just little things. It really depends on what you are talking about "big secret." What we have might be considered big and huge, or it might it something simple but still neccessary to keep secret.
Ok, that is borderline writing my own statement, but that is how I read her comments.
So this big secret could be huge.
A PPU,
An earlier than expected launch,
something magical about the hardware they we don't know yet.
Or it could be something smaller.
The controller now has two big A/B buttons on top.
The controller has a microphone in it.
The New IP "Whatever it Is Revolution" will be out at launch.
The launch lineup
Or it could be something important but ultimately trivial to the gamer
What the costs for games on the virtual console are.
The means that Nintendo allows you to get virtual console games.
I guess the point is not to get your hopes too high on this secret, because it could be the MEGATON!!! Or it could be just a cool bit of information that we didn't know we should get excited about.