Geist 2- with gamepad screen ghost possessions, puzzle solving, clue finding.
Kirbys air ride 2 - with unique gamepad stadium events giving the player that did best in city trial a slight disadvantage.
Lost kingdoms III - even though its not first party, id still love to see it make a comeback, complete with gamepad screen deck management on the fly and tap to activate the cards in your hand during battle.

Just some quick ideas off the top of my head..