What do you think about climbing the 4,000 metres of Mount Kinabulu? You can also climb Mount Trus Madi but it is not as easy unless you are experienced. Or you could head for Gunung Mulu, a UNESCO site which has amazing landscapes. You can go all year long.
Going on a trek in the Malaysian jungle is one of the best ways of exploring the country. The country has lots of national parks to explore and the wildlife that lives in them is amazing. You can go there all year long, whenever you prefer.
Caving is one of the best ways to explore the Malaysian civilisation and find remains of ancient houses and religious sites. Gunung Mulu National Park, for example, is a treasure trove for cavers. You can go all year long.
Malaysia is paradise for divers, whether you are a beginner or an expert. You can go out in a boat or just swim a few metres to reach some superb spots. The best time to go is between September and March for the west coast or between August and September for the east coast. In Borneo you can dive all year long.
Malaysia is full of tropical forests and mountains with numerous rapids that will please canoeists and rafting enthusiasts. You can go all year long, but avoid July and August if you don't like crowds.