EA does not like to play fair when it comes to money, this has been shown in other ways such as online passes, and now it seems they are going to try and control the digital market by releasing the best edition of Mass Effect 3 on their Origin download service only. This was not the case with Mass Effect 2 which was available on Steam and other downloadable services.
You can still purchase the regular edition of the game through those other services, to which you may have become loyal. So if you wish to have the best version you are either going to have to suck it up and buy from Origin or get the even better version at a Brick and Mortar outlet.
The physical copy is indeed better as it not only features all of the content included in the downloadable collectors edition but you also get a physical art book and fabric patch, for the same price of $79.99.