Half and half for me. One of the things I've always liked about Nintendo is that they try new things with each console. Each one has a unique property that was either copied or completely lacking in it's competition. I do not for a second argue that this has always worked out for them! The N64 controller was a complete mess and I'm not especially fond of the WIi's controller either.
The trick is one of utility. The standard PS controller, very much an extention of the SNES controller as Sony and Nintendo partnered to create it, among other things, is standard for a reason. The current layout gives a great many points of input which, in modern games powered by ever more capable computer builds, are giving developers far more options concerning what a player can do in game. But the controller is always the bottle neck.
Take the Wii for example. One of it's biggest drawbacks, in my little opinion, is that it was too simplistic. The motion controll was a stroke of genius though I argue poorly implimented. However, because it lacked a sophisticated button layout that permitted for a great deal of user input, games that would have been fully free on any other system had to be "on-rails" on the Wii. Games like Other M actually had to pause the action to switch to first person mode, which is profoundly unforgivable in an action game, in my point of view.
So, you have a situation where you can either continue the highly versatile standard controller layout, understanding that it is standard for very good reasons, or you can attempt innovation and assume the risks that what you put out may fall short of the standard and hobble creativity. At the end of the day it's all about utility. Shooters are emulating Call of Duty's button control left and right for the same reason platformers emulated the Super Mario Bros formula back in the day. It works, and it works amazingly well. THere are very good arguments for both innovation and adhering to the standard.
