I don't know if anyone's thought of this, but what if the GamePad is used for suit customization? In Super Metroid, you had a menu where you chose what kinda beam you used, what attachment, which suit e.g basically a diagram for the different modules. You could have the same display on the GamePad, but for beams you'd choose 3 other beams (kinda like OoT,) an attachment (shotgun, lazer, long range, ect.,) heavy suits or lite suits ect... You could also use it for 1st Person, but the transition could be iffy. I think it'd be cool to use it when you roll into a tunnel via morph ball.
On the topic of the module screen, I had one last idea. Remember how you could inject phazon into your suit in MP3? What if you could enhance certain parts of the suit? (not neccesarily with phazon.) You push (or tap) a button and that part of the suit and it's enhanced. For example, enhancing the legs increases jump height, jump speed, and speed. Enhancing the cannon would increase weapon damage, rate of fire, and accuracy.
You could also have Samus do partial transformations from zero suit to Power Suit (Power Suit specifically because it's not as bulky as the Varia.) For example, you're dangling from a ledge and the suit grows over your free hand; you then proceed to shoot people on the roof before they can see you. Now, for this to work, it would probably have to be scripted. Scripted in the sense that you hit the shoot button and the game fills in the blanks (kinda like auto-jumping in Zelda or fighting in the Matrix.)