Honestly I think this is alarming for Nintendo, they need software sales to increase though I would blame third parties for a hunk of this problem Nintendo expected them to have software ready for the launch window. Quality software that would sell should have flooded the market by now and it didn't.
As for this "Nintendo isn't taking a loss" or "Nintendo is only taking a small loss" that's bull shit. Nintendo has taken hardware losses in the past and never posted an annual operating loss. When Virtual Boy went down in flames Nintendo still didn't post an operating loss. Lets say the Yen is not responsible for 80% of Nintendo's losses which some media sources suggested was the case. With Wii and DS both selling at a healthy profit and software sales on all platforms also selling at a profit. Despite drops in software and hardware sales across the board their should still be a shit load of profit. 100's of millions of dollars should be made in profits yet Nintendo is said to be taking a loss of 200 mill. That indicates that Nintendo is taking a much larger hit with each 3DS unit then anyone is willing to believe.
As others said WiiU R&D can't possibly be the cause, PS3 barely cost Sony when it was in development and Sony had a much smaller amount of profits to rely on. Also Nintendo's profits have been consistent despite R&D for new hardware in the past. If all indications are correct and WiiU is only 50% more powerful then PS3 and the hardware is only barely capable of using two tablets I'd say R&D shouldn't be much more expensive then the original Wii.
Hopefully Nintendo's Super Mario 3D Land and MarioKart7 both blow the charts away or we have a serious problem. In fact we have a serious problem anyways because without SW sales third parties are dropping support and the remaining supporters in Japan will pull out if their heavy hitters fail to gain any traction!
-JC7
"In God We Trust - In Games We Play " - Joel Reimer
