Played this game for a few years before getting Madden 09 on the Wii and have to admit this would probably still be my current madden game if not for the Wii's motion controls.
As with all maddens they focus one particular new features, which in this version was the 'superstar' mode. This mode allowed you to be your own player within the game. Starting off with picking an agent and then going through the 06 draft. After being drafted you then do practices and games trying to rise up there depth chart, although you can alter the depth chart yourself to make your player the starter. Further into the game you get to decide whether to take up movie roles and do player endorsements. I personally never got this far, I don't think I even made it out of pre-season as I found the game quite limiting and generally boring to play.
The main addition to the franchise mode is the QB vision cone. This basically produces a field of vision for your QB where they can throw accurately. The greater the QBs awareness, the wider his cone. For example Peyton Manning's cone covers almost the whole field. Whereas Kyle Boller's barely covers a 1/4. You can throw to receivers who are outside your cone, but your accuracy drops dramatically, so the chances are you either throw an interception, or the ball will go where your receiver can't catch. This means you have to move the cone so the receiver you want is inside it before you throw, adding an extra element to the passing game and adding that split second that could result in a sack. I found this new feature to make the game feel much more realistic. No longer can you take an unknown QB and throw like Payton Manning. Another element added here is you can now throw over, behind, at the knees or above the head of the receiver by using the control stick when you throw. This allows you to throw the ball to a covered receiver without it becoming nearly an automatic interception, as was the case in previous games, as you can throw the ball where the DB can't get it. E.g. if randy moss is covered by a short CB, throw towards above his head where only he can get it.
The final major addition in this version is the 'Truck Stick'. This works in the same way as the Hit stick on defence which was added in 05. It allows the offensive player to try and run over the defensive player but it increases the risk of a fumble.
The franchise mode is pretty much the same as 05, but with an updated roster. Again the bug exists with IR. Which is when you put a player on IR it doesn't free up a roster spot, which can be very annoying when you have lots of season ending injured players.
The graphics in the wii version are certainly inferior to those of the Xbox360 or ps2, but they are an improvement from 05, which is all you can ask for really with the GC lower specs.
Overall I think Madden 06 is a great madden game, the QB vision and truck stick additions do make the game feel more realistic and add an extra element to the game play. However some bugs still haven't been resolved and the graphics are poor when compared to the 360 version.