I saw this article and i found the idea pretty interesting: http://www.explosion.com/30989/why-the-wii-u-is-destined-to-become-the-next-sega-dreamcast/?utm_source=zergnet.com&utm_medium=referral&utm_campaign=zergnet_57717
I think some important points where missed though. For one Nintendo's first party line-up is much stronger than Sega's was, and so is Nintendo's financial position.
However the Dreamcast final blow was piracy, and recent rumours suggest that the Wii-U has already been hacked. Also Nintendo barely makes an profit on the Wii-U system itself if any, a situation very different to that of the Wii and other Nintendo home consoles.
Wii-U even if it would fail would not force NIntendo out of the hardware market, but could we be looking back on the Wii-U 5 years from now as we do on the Dreamcast?
LOL, Nintendo releases before Sony for once and now it's being compared to the Dreamcast? Wii launched days apart from the PS3 and it outsold the PS3!
Also like you said, Sega was going through a tough time. Dreamcast released 2 years before then PS2 and 3 before the GCN/XB. It entered the 6th gen prematurely, and without much financial backing after Saturns poor sales.
Plus Sega was just entering the 3D gaming industry, and while Sonic Adventure and Skies of Arcadia were excellent games, they also cost a bit to develop and didn't sell that well.
Nintendo will not be hurt by the Wii U, it might not sell as well as the Wii, but remember the PSP had piracy issues too and it sold 75 million units! I expect the Wii U to be Nintendo's second best selling home system, after the Wii, ahead of the NES and SNES. However I do agree, they need to really work on their 9th gen system, they can't focus on Handhelds all the time.