FGR; I think you're referring to the 'Mortis Trilogy'. That is actually one of the few stories in TCW that has some real depth to it. A lot of people thought it was a lot of hogwash, and I can see why people think that if you look at it only superficially. However, there's more to it than meets the eye. Lucas dives really deep into Campbell and Jung here (two of the main influences for the origin of SW). This trilogy can be seen as an allegory for the entire saga, and many people recognized it as such, but it doesn't stop there.
The season in which it aired (season 3) had the title 'Secrets Revealed', and after the season was over many complained that they hadn't revealed any real secrets. However, if you look closely at the Mortis trilogy, and you go with the idea that every story element has its parallel in the saga, then some of the 'plot devices' of Mortis are suddenly rich with symbolism, and actually reveal some 'secrets' about the saga that people have been wondering about for a long time. I personally believe this was Lucas' way to 'reveal' some stuff that he did not like to outright state as a fact. He did it in a way that is open to interpretation, and I think it's very clever. Of course there are many people who won't buy these conclusions for this very reason (it's open to interpretation) or just because they like the EU explanations better (ugh). In fact some of the metaphors have several layers, I really like it. Even though I think the story of Mortis (especially the third and final part in which Anakin 'needs to forget') could have been done better, I think there's some genius in there.
My personal conclusions:
1. The will of the Force created Anakin to preserve the balance. (On Mortis, The Father made Anakin come into the world to preserve the balance - Father symbolizes the (balance of the) Force) So, it was not Sidious/Palpatine who created Anakin. (A popular theory among EU enthusiasts)
2. Darth Sidious is responsible for sending Anakin his visions about Padme and his mother (On Mortis, the Son showed Anakin the future, broke the law of time - the Son symbolizes the Sith)
3. Only one who is balanced; one who performs acts that bring balance will become one with the Force (The Father 'ghosting' upon death while the Daughter did not, even though she selflessly sacrificed herself)
4. The will of the Force is to be in balance
5. The Jedi were corrupted by the war, and partaking in it was wrong; it led to their destruction. (Daughter was corrupted by the conflict, and brought about her own destruction by bringing the sword into the conflict) In this case, the sword symbolizes the clone army as well as Anakin himself, both were 'weapons' that were found in a remote place, brought into the conflict, and ultimately brought about the demise of the Jedi.
6. On Mortis, Qui-Gon showed Anakin the path to balance by telling him to do neither the 'default' light or dark extreme, but follow his instincts and let the will of the Force take shape.
7. In RotJ, balance was brought by a perfectly balanced act of light and dark: a selfless betrayal. Watching the end of RotJ is slightly different with this in mind.
8. The Dark side works like a poison. (On Mortis, Ahsoka was bitten by the Son in disguise)
Now this probably doesn't make a lot of sense if you haven't seen the trilogy. Mortis caused quite a ****storm because people were misinterpreting the concept of 'balance'. (Some people thought it means it's 'okay' to use the dark side every now and then, but that is really not what Lucas is saying.)
In any case, it's a story that sparked an unprecedented amount of philosophical debate on the Star Wars internet, and for that alone it is special.