There are actually a couple of things to consider about all this however. The first is simple: If Nintendo actually hired Retro Studios it means that Retro Studios needs to do the job Nintendo has asked for. That's why they were hired to begin with. To put it more simple, your manager doesn't hire you for a job so that you can do whatever you want. Your boss hired you for your job because you know how to do it... but also because they have certain expectations of what they want. They hired you because they believe you can fulfill those expectations. The gaming industry is no different in that regard. Retro Studios probably had some idea of what they were getting into. And while Nintendo has high expectations (brought on by consumers, mind you, not just Nintendo themselves) by this point in the gaming realm... a developer should know better than this by now. It's not as though Retro Studios wouldn't have known what they were getting into. Nintendo has been at this for a long time. Their name and brand is pretty well known in the the gaming community by now and their expectations are more than well known by this point in time.
Lastly, I think sometimes you MUST let the developer have their freedom FROM the consumer. This means that consumers shouldn't always get to choose. It doesn't mean the consumer is stupid, it means that if the consumer is always listened to it keeps the industry from taking chances and risks that might result in some pretty good games. Likewise, developers ARE consumers as well. To give you an idea, some developers did their best work because they were trying to please the consumer, sure... but they didn't necessarily sacrifice what they wanted to do it. Take a look at Valve who pretty much ALWAYS do what they want regardless of what the consumer says. It doesn't mean they're not trying to please the consumer. But why should they be constrained to just doing what the consumer tells them to do? if that had happened you would've NEVER gotten Portal, which ended up being loved by consumers.
Remember, the consumer doesn't vote with what they say on forums and whatnot... they vote with their wallet. And you know what the consumer is constantly telling the gaming industry? That they want more first person shooters at the moment. Because THAT'S what consumers are putting the money down for. In short, the consumer is just as good at sending mixed messages as anyone else. Gamers complain on forums all the time about the saturation of first person shooters... but they rarely want to buy something else. So what does the developer do? Continue to produce First person shooters because that's what the consumer says he wants? Or take a risks despite that the consumer never asked for that? Some games we would've never gotten made without the latter. Games such as Metal Gear Solid, Uncharted, Castlevania: Symphony of the Night, Final Fantasy VII, Metroid Prime (boy oh boy were consumers pissed when they heard the next Metroid would be in first person way back when), The Legend of Zelda: The Windwaker, Disgaea, Final Fantasy Tactics are just SOME games that would've NEVER been made. Why? Because consumers never ASKED for these games. In the case of The Legend of Zelda: the Windwaker, Metroid Prime, Kingdom Hearts and Castlevania: Symphony of the Night... upon their initial releases it was almost a certainy consumers DIDN'T want these games. But they were given to us anyway in hopes that we'd like them. I recall in the midst of the late 90's walking into a game store where I found a stack of Castlevania: Symphony of the Night. When I asked about it the clerk told me, "No one wants it... it's not 3D." Because at the time that was the Playstation's selling point. It provided 3D visuals, right? So a bunch of people got rid of their Castlevania Symphony of the Night game because it wasn't 3D and because, at the time, it was described as not being a "real" Castlevania (it was the first Metroidvania, after all). The consumer basically said to Konami... "Don't give us THIS thing!" But a couple of years later it became one of the most highly sought after Playstation titles of all time. Being labeled a Greatest Hits and garnering one of the largest cult followings of any game the Playstation ever had. Final Fantasy Tactics was only conceived because Sakaguchi was a fan of Yasumi Matsuno's Tactics Ogre... a game most territories outside of Japan had never heard of... and initially Final Fantasy Tactics didn't exactly catch on either.
And the last and most obvious thing... consumers are a HUGE group of people. You can never please all the people all the time. You can't even please all the people some of the time. You can ONLY please SOME of the people SOME of the time. Again, because the industry is a business the only way that developers know they're doing alright is dependent on how much the game sells and word of mouth. It's not like most developers are looking to sell as many copies of their game as Grand Theft Auto IV. Most of them know that achieving THAT with their game is a long shot... because that success is already unusual as it is (remember, Rockstar can't duplicate that with ANY other game they have outside of the franchise). Some developers, such as Atlus, only care about recovering the losses spent on making the game (Atlus considered Catherine a success long before it sold a million copies, for instance--they claimed to have made their money back just after the launch in the US). It's easy to latch onto this idea that, "If the developer just developes a good game it'll sell," but the truth is, regardless of the consumer... you still have to find a way to sell them that game. You have to make the conumer WANT that game. And not just because the consumer demands it (the consumer is too broad a group for the industry to satisfy every last one... so they typically go after a specific audience... Final Fantasy isn't the designed for the Grand Theft Auto fan for instance) but because you have to convince them it's worth investing their time in. And doing that with new and unfamiliar franchises in this day and age is hard. Almost not even worth the risk for developers. Because if you spend 100 million dollars to make a game... you want to recouperate that 100 million dollars to that it can (hopefully) go toward another gaming project.