I don't think Nintendo will go with flash cards, they are still pretty expensive. If anything I think it might be the generation where Nintendo uses a mainstream format (bluray). The DVD has been maxed out with the xbox 360, there is no room left at all. With the next Nintendo system being much more powerful than either the 360 or PS3 (i'm assuming) they will need more storage space.
I also think Nintendo will use an SSD instead of a hard drive to consume less space and less power with faster load times, in 2012 SSD prices should be very reasonable for something like 120 GB.
I like your idea of wireless LAN for the next system.
Nintendo said they tried the Natal interface and didn't like it, I would imagine their next controller would be similar in design with the wii remote, only with the latest and greatest accelerometers and gyroscopes for better accuracy.