What policies would those be? I'm genuinely asking. My bet is that Activision and EA, since they are "big dogs," are looking for a better royalty rate than everyone else gets.
Essentially you nailed it royalties and fees, front page exposure, marketing exposure etc.
Sony and MS give more leeway to these big guys. It's also why a lot of indies like Nintendo because Nintendo gives them equal exposure and footing. So it is a double edged sword.
The point still stands though, if you are an Ea, Acti, Take Two or Ubi who are you going to work with? The company or companies that make it easier/cheaper for you to publish or the one that doesn't? If putting DLC on the WiiU costs 20% more to put on the eshop than it does on PSN/Live And you are going to get less sales, then where is the incentive? Same goes with Digital Releases.
It is up to Nintendo to make it an environment where 3rd parties can succeed and be profitable and to do that they need to have internal policies that make their system open and accessible.
This goes for VC too. There is clearly an additional cost/barrier to entry that makes it not profitable enough for companies to release their back catalogs of NES/SNES/N64 games etc on the VC and part of that are Nintendo's policies. There are no other explanations. Just think it through. It costs X for a developer to put in in VC format, costs Y to have it rerated, and then B to pass Nintnedo's submission process and then after all of that they have to give up a % of the sales. Nintendo can facilitate all off that to the benefit of both parties by making the easier/less restrictive to get a title running in the VC, offer development tools for little or no cost, fast track submission and or wave fees or lower the % cut of each sale. Or they can do any combination of this. The goal is to generate more support for their system and to get more games out.
It is clear though that Nintendo believes that they just need to sell more systems so that publishers couldn't ignore the user base and would be willing to put up with fees and policies that aren't conducive to higher profitability. They are quoted as saying this much and it clearly points to a deficiency in policies and management that they aren't willing to make changes to fix the situation.
Don't get me wrong I love my WiiU I own or have owned more games for it than most folks and will buy more going forward, but it is painfully obvious that it is Nintendos own internal policies that prevent a lot of games/DLC and support from coming to the system especially in a situation where they need as many games as possible on the system to help facilitate a healthy user base.