I love Penang. It is a little island but therein lies its charm.
It has some beaches and if you have time there are some lovely little islands not far away that you can go cruising through.
It also has some hills and a bit of shopping and a few temples etc.
There are a few differant cultures living together there (Malay, Chinese, Indian) so there is a great variety of yummy food.
I guess it depends what you're after. For me Penang is a more authentic Malaysian city. KL could be just about any big city in Asia (and it certainly doesn't smell like Asia in most parts) and for me that's it's problem - it's kind of bland.
So if you want to visit a city and go clubbing and shop in department stores/brand shops then KL's your place but if you want to slow down a bit then Penang might be better.
You could always fly into KL then travel by train up to Penang then cruise to Phuket and fly out...