I guess the problems come with the fame. As long as you are a small site, you can do pretty much whatever you want, but as you grow, you have to compromise in some way. You can bend to advertisers and lose some of freedom, or go down the chan way and get a name that reflects what you have to offer and probably have a revenue that is consistent with that.

On top of that , there's the fact that the average user, simply doesn't care about all this freedoms or number of upvotes and stuff like that. They just want content and reddit right now has enough for everyone.