Re: OP. I'm generally a fan, and I've known people who've lived over in Thailand for years and have never been to Malaysia...the think it must be like Saudi Arabia or something.
The Borneo areas have been fun and interesting, especially Kuching and a trek to the lower Kinabatangan in Sabah. Also Labuan and Brunei. I like the Perhentians a lot off the east coast of the peninsula. KL is somewhere between Singapore and Bangkok, but the prices are much more like Bangkok though it'd be nice if taxis were more like Singapore.
Lowlights include Johor Bahru (terrible example of a city chopped up to serve the automobile) and I'm also not a fan of Georgetown. KK is also pretty bland but was leveled in WWII.