Their biggest problem by far was going for an audience that no longer existed. The very same audience who spend no time on internet forums like us and discuss gaming articles and news. Even if the media part had been perfect; it would likely not have changed much since they still aimed the core product at a target that was simply not there.

The media coverage+marketing arguments have some merit, but are not the whole story, or even a huge part of it. Nintendo's biggest problem was failure to keep up with market movements and respond accordingly, the Wii U is the ultimate showcase for this train of thought.

If poor mainstream and gaming press was all it took to condemn a company or send them into obscurity or major financial troubles, Microsoft would be circling the drain decades ago, but they're still going strong. The One is even selling fairly well, despite being aimed primarily at bro's and nerds like us who throw more hissy fits at the failures of these companies.

The reasons Nintendo is getting more criticism by people like us, and most others, with the Wii U compared to the N64 and Gamecube are quite clear from where I'm sitting. First off; more people have access to more news, in the N64 and early GC days, internet was still alien to most and gaming magazines were the primary source of information on gaming related news. Secondly; despite low hardware sales, the N64 and GC were both known to sport great gaming libraries, they even had decent 3rd party support at the time.
Third, and most important for the mainstream media; Nintendo were still making profits on the N64 and GC and was considered a stable company despite having tumbled from the NES/SNES throne a few years prior, the Wii U and modern day Nintendo have crashed on almost all fronts and posted several fiscal years in a row in the red, lost almost all influence and have even experienced their handheld to suffer a serious decline, they also released two consoles in a row that lost them money at launch.
The N64 and GC days are far from as bad as present day for Nintendo, it's no wonder media and consumers are picking up on this.
Besides; we can't rightly say that there was a lack of fire and brimstone directed at Sony when they made fools of themselves with the PS3 and started bleeding money either, can we?

depends what kind of bad press. calling a company out for stealing ideas (MS) and whatnot isnt the same as calling nintendo doom and out of touch company all the time and also i fail to see how you can even make that comparison since MS literally has no  real competition.

in the GC days the internet was pretty much the same except now theres more ppl but that does not make a difference here since theres only so much ppl talking about gaming on forums. as for other media gaming news sites only (ign etc.) its also pretty much the same as it was in the GC days. 

also you cant predict what the mass market wants next.

For those, who are interested, here is Nintendos Place in the list over time:

Maybe you were just younger back then and didn't notice it but the GameCube took a ton of flak, lol. When PSP was unveiled and it looked like Nintendo's hold on the portable market could be slipping a lot people were all over Nintendo.