Didn't Windwaker only have 3 dungeons or something? The two abandoned dungeons would have kept it on par with OoT and MM, without them it seems like you're being shortchanged. Sure, the Twilight Princess style went down much better with the fanboys but you can't pay too much attention to the overly vocal minority that hated Celda.

Nobody thought to blame CD-ROMs as Sony made a big success of it, but sticking with cartridges let Nintendo differentiate themselves from everyone else and ensure they were the only genuine alternative to Playstation. In general Nintendo's business strategy can be described as: a) do something different b) never bet the house. The first ensures the potential for runaway hits like the Wii or DS, while the latter ensures they can always try again next generation.