Personally I like trains. They are usually comfortable, you can get up and wander around, there is food available normally, you can read the paper or a good book, and the views are better than from buses. And there are toilets. But they are more expensive than buses although sometimes there are reasonable deals, particularly if you book in advance.
Trains from the deep south arrive in Oban, Fort William, Mallaig and Arisaig. The Scottish network is run by ScotRail. The trains start from Glasgow Queen Street Station, often splitting at Crianlarich with one half going on to Oban and the other to Fort William and then on to Mallaig. These two routes must be amongst the great train journeys of the world, certainly of the UK. The trains may be slow, creaky and squeaky, and somewhat eccentric, but the countryside is outstanding, both to the left and right. Lochs give way to mountains to moorland and back to lochs, both freshwater and sea lochs. Wonderful! Why worry, join the slow movement (unless of course you happen to be on business). The train crew are friendly, they seem to know many of the passengers, and everyone is ever so relaxed. One problem is that there are not that many trains, and sometimes there is no trolley service, so best to be prepared. And they are becoming more and more crowded.
Getting off at Connel Ferry, the stop before Oban, is an option for say Dunstaffnage, but there is no taxi rank so you might as well wait until Oban. On the Mallaig line you can get off at Arisaig and easily walk down to the anchorage.
A treat in the summer is to take the Jacobite steam train between Fort William and Mallaig, real little boys' stuff, and big boys' too.