I should add that this is typical of the style of Marc Platt. I have no doubt that Platt is one of the most gifted writers to work on Who. If you have a chance to catch his Big Finish stories, they really are sublime. As was stated in another thread, this was originally Lungbarrow, the story about the origin of the Doctor which Cartmell and JNT had been working on as the climax to (what everyone believed) would be the last season of Doctor Who. Then, JNT had a meeting and was given the impression that there might be another series.. so they redrafted it to make it a story about Ace instead. I think, therefore, that by going through so many re-writes, the essence of the story become changed. It became more of a fable, viewing the Doctor through the prism of Ace and (as Nyki says) reflecting on the nature of life, death and belonging. It's not an episode that is easy to watch and, I think even the most die hard of Platt fans (of which I count myself one) accept that its difficult to follow..
But actually, thats part of what makes it such a great story
