How long are you going for and what do you like to do? I think Malaysia can give you a really good and varied holiday and is much cheaper than Bali and Singapore (though if you really want to do Singapore you could spend a few days there). I'd suggest the following itineraries that you could mix and match as you'd like
Kuala Lumpur - up to one week (spend time relaxing at hotel with a pool, go hiking at FRIM/other rainforest areas, visit the bird park / botanical gardens, check out the museum of Islamic arts, go shopping at one of the malls, go to the aquarium, see the petronas towers, visit Menara KL, visit temples, go shopping at central market for nice souvenirs)
East coast islands - 4 days 3 nights scuba diving/snorkelling in clear water with lots of fish (note that the east coast islands of Redang, Perhentians and Tiomman are in a marine park so there's no water activities like jet-skiing etc.)
Borneo
- 2 days 1 night at Sandakan visiting the orangutan sanctuary and sun bear sanctuary
- 2 days 1 night visiting the Kinabatangan river to see animals in the wild (I really recommend doing the non-wildlife activities as well like batik painting)
Penang - 3 days 2 nights exploring Georgetown. You can see temples, eat local food, go up Penang hill, maybe visit a water park (Escape Penang might appeal to your teenager)
Malacca - 2 days 1 night wandering around. In my opinion similar to Penang but not as much to do
Langkawi - up to one week beach holiday. It's not a marine park so you can do sea activities like jet skiing, banana boats etc. You can go on snorkelling trips but its a real trek and the quality is not the best. There are non-beach tourist things to do in Langkawi like the cable car, feeding eagles, boat rides through the mangroves.
Let me know if you want any more information about Malaysia!