To add to why I think it's a bad idea... you only need to look as far as the current generation of consoles and their control schemes. The PS3 and the 360 largely share the same library. Why? Well, just look at the controllers. They've got the same number of buttons, and they're roughly in the same place on the controller. It's very easy for a developer to port as far as controls are concerned. Now look at the Wii. I mean obviously the system itself is grossly underpowered but trying to port something to a completely different control scheme is impossible in some cases. Yeah, there's the regular controller you can get for the Wii, but it just goes to show you how much of an impact a different control scheme makes.
Now, they're essentially removing 1 button from the controller for the PS4(unless the PS button functions as Start and Option functions as Select, or Option functions as both). If Microsoft wants to keep this ease of porting, they're going to have to remove a button too from the 720. What's the alternative? Either developers ignore the PS4's lack of the one button and force players to go through a menu to hit Start/Select or however they decide to do it(which, depending on the game's use of those buttons is going to have little impact or it's going to be a nightmare if the game is heavily reliant on them), or they pick the PS4 as the standard and dev their games around the fact that this is how the control scheme is going to be(with the one less button), which offers more limitations than how things are now.
Let's not even get into the touch pad. If Microsoft includes one on their controller too, then more games will use it, and again, games will be easier to port. If not, then it's pretty much going to be for PS4 exclusives or extra bonuses for the PS4 version of a game. The more proprietary things are, the more difficult it is to port something over(or impossible altogether, as the Wii learned). With the way the budget is for game development, I don't think many companies can afford to release their games on a console exclusive basis.