A Gameinformer monthly article "Good, and Bad" on Nintendo and third parties touched on the third party problem. The way the paragraph put it, it seemed to be a mix of several things. One developer said that they're willing to develop for it, but not until it starts to sell better. Which makes sense, why put out a triple A game for an audience sub 5 million (considering a lot of triple A's sell more than that, it would take the entire Wii-U audience buying a copy to = normal PS3, and 360 sales). Another said they could put their game out on the system, but just didn't see it as being a worthwhile venture worth the man power. Another said they wanted to, but Nintendo wasn't reaching out towards them.
I think Nintendo's just stuck in the past, relying on namebrand power (not just the console, but games like Mario, and Zelda). They still don't understand the importance of hard drive space, especially in conjunction to downloadable titles. Which is going to put them very far behind considering the PS4, and 720 are going to probably have 500GB minimum. That's going to lock Nintendo out of several big titles as is.
Then I think they underestimate the importance of online. They still haven't straightened out their friends system. MS has proven Live is a cash cow, and this generation in particular has shown that ppl like online gaming. Nintendo once said that ppl demanding online services are just geeks, and otaku's. I think that philosphy is biting them in the ass right now.
Then, as you said, the marketing is a disaster. Nintendo gets everyone used to a different name each console, or atleast makes it a clear indication that it's a new system. Then they go peripheral crazy with the Wii, and act surprised when ppl think the Wii-U is another add on. They are so profitable, yet failed on so many levels when it came to marketing their next money printing machine.
Not to mention that now they're competing for the casual crown against a growing mobile gaming market. That even if it's more functional, chances are a touchscreen isn't going to grab the attention of the mainstream casual gamers as much as motion controls did (considering every pad and phone has one now, and the PS3 can do it with a Vita, and PS4 has built in touchscreen, amongst other features as well). When you add all of this up, I just don't see the Wii-U pulling Wii numbers. I'm not saying it will be a Gamecube, but they do need to do some damage control quickly. With the PS4, and Nextbox getting a lot of buzz, this isn't a position they want to be in at this point in time.