It clunky, it's the way it's made. Design flaw - probably not. Box is made to a cost and an acceptable level of performance. Toyota decided to use the gearbox, they must have tested it before buying.
My Supra gearbox was much much worse on a car costing twice as much as the IS200.
Design issues don't have to be fixed by a manufacturer, a fault has to be fixed if within the warranty period.