All things considered, I'll agree and say that your time is better spent flying, but that said -- while the road from Singapore to KL is indeed deathly dull and getting around in KL is a bit of nightmare, parts of the road from KL to Penang are actually rather scenic, Ipoh makes a nice stopover (for the food alone, mind you, not much else to see), and Penang is one of those places where having your own wheels is very handy. So if you like driving and aren't intimidated by "Asian" driving, you might want to consider flying down to KL, sightseeing there for a bit, and then driving up to Penang.

And yes, you can do one-way rentals, I've done precisely this (pickup in JB, dropoff in Penang) with Hawk Rent-a-car, the surcharge was minimal and the service was excellent: we dropped it off straight at the airport. However, cheap rental cars in Malaysia are all Protons, and you need to pay a bit more to get a decent (read: non-Malaysian) car.