As you can see it's a matter of choice. I have taken an overnight sleeper train, as a well as a daytime train. If enjoy the countryside and you want to see the countryside, a day train is good. If you want to save a night of hotel expense, the sleeper train is good. Plane is faster, even including travelling time to and from the airports. Keep in mind the extra cost of transportation to and from the airports.

I liked the First Class overnight sleeper train. The cabin has a attached bathroom and shower, but you don't see any countryside.

Bus is fatser than train, but customs and immigration are smoother by train than by bus. What I liked about travelling by bus is the stops that the bus makes at rest stops where you can sample local food in Malyasia.