I think the thing that strikes me in the prequel films is a general lack of real themes. I mean technically you could see something about the supposed dangers of attachment and perils involved with giving authority more power in a crisis, but both are done so poorly or done with so little on screen evidence that they just feel half-assed. Not to mention that love as a general force (no pun intended) good became such a strong element in the original trilogy that treating it with such suspicion in the prequels feels out of sync.
I myself have happened upon two critical themes of alternate prequels which I do think will still resonate with the original films: the importance of being connected with all as those around you, and the inherent dangers of losing one's idealism by giving into cynicism and pessimism.
Both Obi-Wan and Yoda speak of how the Force is an energy field created by all living things, binding the universe together and making it grow. This connectedness is about as critical to the Star Wars mythology as anything. Its something that applies not just to the force, but to people. Luke, Han, and Leia grow closer over the films, the Rebels are named specifically as an Alliance between peoples against tyranny, and Darth Vader himself is the very picture of being cut off and detached from all those around him given his state as more machine than man.This bond, this engagement between regular people is something that means just as much in the prequels.
The growing divide between Anakin and Obi-Wan due to their respective flaws proves to be the downfall of a great friendship. The average Republic citizen's sense of feeling out of touch with the Senate brings about growing unhappiness and a chance for Palpatine to gain power. Jedi and specifically Yoda's seclusion away from the rest of the galaxy proves to be their undoing as they lose their connection with the living and are surprised by the power of Palpatine and the treachery of one of their own. Anakin's severed attachment to his wife and unborn child (due to their apparent death), the family that kept his own dark instincts in check, proves be his tragic push towards the dark side.
Eventually the galaxy's descent into darkness is ended by the heroes being connected to one another. Luke leaves the secluded Tatooine and becomes part of the larger world. The Jedi's (Obi-Wan, Yoda) isolation finally ends with their teachings to Luke, the children of Skywalker (without knowing it) become stronger once reunited, and even Darth Vader moves from being a willing apprentice of Palpatine to a rebellious pupil offering to overthrow him once he discovers his son is alive.
The other major running element is hope and idealism. The Republic (much like America in the era prior to Star Wars' release) is one made of cynical views towards government and in many ways each other. The Jedi don't get heavily involved with Republic affairs, believing they'll simply be part of petty politics. People continually show heavy skepticism towards Jedi knights and the powers they use, neither of which they've really seen.
Anakin's defining trait by contrast is his overwhelming belief that he as a Jedi can make a galaxy a better place. Its this aspect that makes him among the greatest of the Jedi, precisely because he embodies the spirit of being a guardian of peace and justice better than anyone. And its this fact that eventually makes his fall so tragic. Because Anakin's story is continually one of sacrifice: Leaving his family on Tatooine and likely not being able to come back given Owen's grudge. Not expressing his feelings of doubt and internal struggle to his master because Ben had placed so much faith in him being a great student. Seeing his own wife less than he could because his role in the Clone Wars was so critical. Being able to move on from all the good people he's seen die in this war.
And he does these things even with all the lonely nights, fallen comrades, and troubled thoughts, as he still believed in the good intentions and ability of the Republic and the Jedi to bring justice to the galaxy. Because he still had faith. But once he believes he's lost his family... its the one sacrifice that was too much. Once they're gone, the Darth Vader in him, the one who had continually said that ruthless measures would get real results and that more power was necessary to bring true justice to the galaxy, he murders Anakin. There will be peace by his hand at any cost, and he will create a world where no innocent people will be destroyed thanks to those starting a war.
This loss of optimism ultimately affects Yoda and Kenobi as well. Both believe that Luke must destroy Vader, as there's nothing left of Skywalker in him. The Clone Wars and their terrible consequences leave the two unable to see the real power of Anakin's son lies in his love and forgiveness. The "New Hope" Luke represents is ultimately the one that brings back faith and idealism in others; from a scoundrel like Han to eventually his own father. Luke's very existence changes Darth somewhat, though his offer of power to Luke in ESB shows how Vader's still distorting Anakin's sense of justice.
But in ROTJ, Luke's demonstrates love and faith in his father; tossing away his lightsaber rather than destroying him even though it would be so easy and understandable for him to do so. Its that moment in which Darth Vader dies, because his entire belief in callous ruthlessness proves to be wrong. Anakin Skywalker is reborn, and upon feeling genuine belief for the first time in decades, sees Palpatine for what he really is, and saves his son, just as he saved him.
Hence we come full circle. The loss of idealism by the Jedi is undone by one optimistic young man who still believed in spite of it all. Over three movies Anakin Skywalker lost all hope. And over three movies, thanks to his son, he regained it.
To me, having these themes doesn't just explain the original trilogy, it enriches it.
