One of the patterns that stands out to me in the broad view of penguin evolution is that their skeletal adaptations seem to have proceeded from the ground up. By this I mean that even the earliest penguins that show up in the fossil record have very short, stout feet. Over the course of penguin evolutionary history, wing bones later continues to flatten towards the perfect flipper shape, the shoulder girdle reorganizes itself to accommodate more powerful upstroke muscles for diving, and finally cranial changes related to modified feeding preference show up. In a simplified sense, the skeletal changes proceed toe to head, rather than head to toe. So why the short legs? Hind limb morphology would seem to be an afterthought for a flightless diving bird. In fact, reducing the length hind limb is advantageous for many reasons, including cutting down on drag while swimming. Penguins can also use their short broad feet as “rudders” to aid in turning. A short leg is also useful in conserving body temperature in cold climates, although the earliest penguins probably did not need to worry about this very much given they lived during a much warmer time in Earth history.
How do these short legs effect movement on land? Some early scientists had proposed that the waddling gate of penguins, alternatively considered awkward or endearing depending on your point of view, wastes energy. As it turns out, waddling is actually an energy saver. In 2000, researchers Timothy Griffin and Rodger Kram conducted studies on shuffling penguins and found that the weird way they move makes sense metabolically. Essentially, as a penguin waddles side to side, each sway stores energy for the next step, somewhat like a pendulum. By measuring the force generated with each step using a special platform, the scientists determined that penguins conserve about 15% more energy between steps than humans. Thus it turns out that the short feet of penguins are not the most efficient set-up, but this inefficiency can be partially overcome with a novel gait.
You can really see the side to side motion of the penguin waddle in this video:
Griffin, T.M. and R. Kram. Biomechanics: Penguin waddling is not wasteful Nature 408, 929.