You should fly one way and take the bus the other. e.g, fly from Singapore to Penang, then take the bus to KL and the bus from KL to Singapore.

Flying Penang-KL-Singapore doesn't make logistical sense, given the time required.

Also, the buses from KL to Singapore are some of the most comfortable in the world if you take upscale lines like Transtar's First Class service. Only one seat on either side of the aisle, video on demand, meal service at your seat, enough leg room for even the tallest people to stretch out comfortably.