If your (or wife's) current comfort zone is to approach the SE Asia explorations step by step from infrastructure/facilities most advanced (Singapore) to most primitive, then I don't see anything wrong with the idea of making Malaysia the next country of focus. That's pretty much ratcheting down just one step.

However, I would suggest that peninsular Malaysia with is maybe more suitable for a 7-10 day trip (Melaka, KL, Penang, Cameron) or perhaps two different long weekends. In other words, maybe not the best match for a 2-3 week trip where there is no desire to put a beach resort like Redang or the Perhentians in the mix.

So I'd suggest instead going to East Malaysia--Sarawak (via Kuching) and Sabah (via Kota Kinabalu) Scenery, culture, orangutans, villages, etc. And a 2-3 week time frame would be perfect. Infrastructure and support as you wish, no need to "rough it" unless you specifically want to and choose way off-the-beaten track locations. Should be able to get some budget flights from Singapore to/from these locations.