The overwhelming "missing thing" for me in the PT was the ensemble cast feeling - the "Team" camraderie of the OT. In the OT, you really care about the core characters, and a lot of the story (especially in Ep V & VI) comes FROM the characters.
It would've been neat for me personally to see (a slighter older) Anakin become a Jedi in Episode 1. His first mission with the "Team" (Ob-Wan & other Jedi) would be the exciting climax battle of Episode 1.
He would fall in love with Princess Amidala in Episode 2, but rather than moaning about how they're "holding him back" he would actually choose the Jedi order OVER the Princess as the clone wars start to kick off. After spending one night with Padme, he'd take off on his "damn fool mission" with Obi-Wan and the others. Padme would be very upset with him, but we'd see that his ambition to lead the Jedi team to glory outweighs anything else. The "Team" mission in Episode 2 would end in disaster, with Anakin carrying the can due to a fatal mistake he makes. This downbeat ending would echo Episode V's, and would set the tone for Episode 3.
Episode 3 would play out with Anakin's move to the dark side, following him being "demoted" by the Jedi Order after his failures in Ep. 2's mission. He is motivated by power & greed, not love. By this time, we should really care about the other Team members (how great would it have been to develop these Jedi characters rather than spending hours in the Senate/Padme's bloody veranda.....) & when Anakin finally betrays them it would actually have some emotional resonance - he is supposed to have their (collective) back, but stabs them in it. Anakin sees Padme one more time (like King Arthur visiting Guinevere before his last battle) and asks her to join him. She refuses and he simply leaves her, to go and face off with Obi-Wan. He has no idea Padme is pregnant. Obi-Wan punishes Anakin for his betrayal and the murders of their friends/team mates, with dialogue that rises above the existing Episode 3 "ya-boo, the Jedi order sucks, from my point of view..." stuff.
In this version of the PT, the background characters would become just that, BACKGROUND, not central characters sitting around in endless councils, senate meetings etc. The core characters would be "Team Jedi" and so we would get the ensemble feel of the OT, with their adventures played out against the backdrop of the creation of the Empire & Anakin's disintegration into becoming Vader.
Just my 20 cents!