The Metro Kingdom looks to be an extremely well-developed, prosperous province whose residents have known peace, balance, and the feeling of a full belly for centuries on end. It's reasonable to imagine that this has lead to increased bodily developments in the native population, hence their freakishly tall stature.
But Waluigi's own strange stature is not to be measured against the Metro Kingdom constant. He's a freak of nature even by the standards of a Homo nintendonus (Mario's purported species). Whether this should be spun into a positive or negative is up to whoever.