Shhhh we're not supposed to let them know yet

Oh the irony!!!

I have to agree with padib here.

There's absolutely nothing wrong with criticizing Nintendo for bone-headed business decisions or unreasonable sales goals, or for going its own way as the industry shifts in the opposite direction (although that's something I admire about Nintendo, personally).

But there is an undercurrent of disrespect and bitterness beneath much of the criticism (not all, but some). I truly believe many video game enthusiasts are still frustrated about the success of the Wii because it was, for lack of a better term, a "softcore" console. I also believe that Nintendo's philosophy of design -- relatively underpowered, family-friendly, and local multiplayer-focused -- offends the sensibilities of these same fans.

Nintendo stocks jump 20%, no one cares, Nintendo announces high 3DS sales, no one cares, WiiU has highest selling month in USA, no one cares, Nintendo becomes bigger than all of Sony,no one cares, but when Nintendo slashes predictions, stocks fall, announce that they EXPECT a 250m loss even though their competitors lose a lot more and more frequently, it makes headlines.

what is the root of all this bias against Nintendo? Is there a particular reason like Nintendo not paying for positive press or is it just the cool thing to do?

Where?

There!

Saying the games have charm is very different from the company itself having charm. 

Is the same when people say Disney movies have charm, or like games like Jak & Daxter or Little Big Planet have a special charm. That doesn't make people have a special love for the company.