The truly timeless villains are defined by their versatility. They can be used to depict a variety of archetypes without contradiction. Here their motives are simple- there we see shades of something deeper beneath the surface. Now he plays the role of card carrying villain, now he plays the role of well intentioned extremist; the magic is in making both characterizations believable.
With Eggman it was always straightforward because his ruling character traits are his monstrous intelligence and his even more monstrous ego. What good he could obviously do with the one highlights the evil he carrys out because of the other. His greatest virtue is the root of his greatest sin.
The Penguin is another villain whose timelessness stems from his versatility. Unlike the rest of Batman's rogues gallery he's largely remained in the mold of Silver Age/60s tv series super criminals, enacting complex bird themed crimes to outwit his nemesis and prove his genius. While his methods have gotten more cruel, his modus operandi is largely unchanged. Because unlike most of Batman's other enemies, The Penguin is sane: whereas they commit crime compulsively, he chooses to act the part of a villain because he enjoys it. And indeed The Penguin is an actor; he revels in the theatre of gentleman thievery, the drama of the chase. It's all a game to him, and that simultaneously makes The Penguin more innocent and more despicable than the average Batman villain.
Quote NachoThePikachu :
I WILL BE AN ADMINISTRATOR, RULING OVER CHAO ISLAND
except it WON'T BE CHAO ISLAND ANYMORE
IT'LL BE BANANA ISLAnD