Upvote:6
Rail wins out for ease-of-use, comfort, and scenery. Every city you mention is accessible by rail. You would have to transfer to bus only to get over the bridge from Kyle of Lochalsh to Skye. Rail is generally faster and more comfortable than bus - much faster and more comfortable on main lines, slightly more on secondary lines; and the scenery is usually better. The chance of going over one of the great railway bridges of Scotland is worth taking the train alone.
I don't know about cost, but I would imagine that is where the bus would win out.