Well, answered questions from the OT are now:
1) Where did all the stormtroopers and military might of the Empire come from?
2) How did Palpatine gain control over it; where did he come from?
3) Where did Anakin Skywalker come from? Who was his family?
4) Why did Anakin not take well to Jedi training? How could someone capable of being a Jedi go bad? What were his motivations?
5) If Obi-Wan was so great of Jedi, why couldn't he deal with training Anakin?
6) Who was Luke and Leia's mother?
7) Where did R2D2 and C-3PO come from?
8) What was this mysterious Jedi Order and who were the Knights of the Old Republic? How did they operate?
9) Why did the Republic fall? What could have been done about it?
10) What were the Clone Wars?
11) How did Luke end up living with Owen and Beru?
12) How was Bail Organa involved, and when was Obi-Wan a General?
THE ANSWERS FROM TPM and AOTC:
1) Stormtroopers are probably Clones with armor that has evolved away from symbols of the Old Republic and has been replaced by symbols of the Empire. As the might of the Empire strengthened, Stormtroopers could also include enlisted and drafted random humans from across the galaxy, as time went on, and it hasn't been denied. But it's been pretty obviously answered for the most part.
2) Palpatine was the Senator from Naboo, and he most likely acted as Darth Sidious to set up a situation he could capitalize on politically, and did so, gaining emergency powers as he innocently protested that democracy could work in the face of the greed of special interest groups from "corporate galactica."
3) Anakin was a 9 year old slave boy, son of Shmi Skywalker, another slave. He had a dubious virgin birth, which may or may not be true, but he grew up wanting respect and trusting in his own ability to achieve goals and disciplines that he set for himself. To survive, he learned to cheat around the rules.
4) Anakin knew his mother and wanted to save her from slavery, and end its injustice as he saw fit. More of answer 3 lends to this answer. He also lost his mother, and had difficulty dealing with Jedi restrictions against unsanctioned missions, personal indulgements, and revenge. We saw that just as he could not blame himself for his slavery condition (which was true), he learned to never blame himself for his failures to either a) accept the Jedi training conditions and their consequences for his mother, and the lifestyle he'd chosen or b) accept that it was his fault, that bad things would happen that would terribly affect him, if he strayed outside of the rules Obi-Wan laid down for him - hence he winds up in an ultimately tragic relationship with Padme. Her fate, no doubt completes his downfall. But yes, he always only wanted just to be of help, do good, and be a hero.
5) Obi-Wan was a strict adherent of the Jedi code and didn't want Anakin and the responsibility of training him. But Obi-Wan's master, Qui-Gon, was the student of Dooku, a rule breaker, who taught Qui-Gon his own interpretations or dismissals of what was important to the Jedi code. In the end, Qui-Gon was killed, and Obi-Wan, barely ready to be a Knight, was charged too young, with being a Master to a boy who was too old to begin the training, due to Anakin's previous life experiences, discussed above, as well as Anakin's attachments to others he loved. Qui-Gon probably could have trained him, though Dooku could have remained a danger. We don't know when Dooku really thought of joining the Sith yet. Of course, Qui-Gon, had he lived, would have been susceptible to Dooku. Obi-Wan, however, was only too green and inexperienced to deal with an apprentice only 15 years younger than he was. In most societies, 15 is too young to become a father, yet a young father can handle it in various cases, because the child is a baby in a crib, dependant on the parent, not a podracer with a knack for finding trouble and powers they cannot control. It was doomed from the start. The only new question remaining is how much of this did Palpatine know or plan?
6) Padme Naberrie (Amidala) was Luke and Leia's mother. She was the Queen of Naboo, therefore giving Leia official inheritance of the title "Princess."
7) C-3PO was a junked protocal droid that may or may not have known R2-D2 before being scrapped and having a memory wipe. Anakin Skywalker found what was left of him and rebuilt him and gave him his name we know him by. R2-D2 was one of 6-8 astromech repair droids purchased by the Naboo to serve Padme Amidala's royal starship in basic and emergency maintainance. He is the last survivor of his droid crew from the Trade Federation conflict, and become an honored and trusted servant of Pamde's. The droid's union as counterparts was completed, upon Anakin and Padme's union in marriage.
8) The Knights of the Old Republic were governed by a Council of 12, including Mace Windu and Master Yoda. They maintained an ancient temple to their order on Coruscant, which was at least 1,000 years old, possibly 3,000 years old (Nomi Sunrider had the Jedi based on Exis Station before choosing to move them to Coruscant, years after Ossus was destroyed in the Sith War). The Temple has training and living quarters for younglings, who are taken close to their age at birth, to be raised in an ideal and sheltered lifestyle, until fully inculcated into the Jedi Way. Knights roam the galaxy on a life of continuous missions. They normally choose from younglings at age 13, to become formally apprenticed for about 10-12 years, with one Master. They become Knights themselves at around their mid-twenties. Most Jedi Masters training apprentices would be expected to be older than 30 (for a human master). Very old Jedi may live in the temple and serve on the Council or act as librarians, and other specialists. During the Clone Wars, it was asked of all Knights to become Generals, and their older Padawans to serve as Lieuteniants, commanding Clone Warriors and Republic officers against the Separatists. Jedi who could not be trained to become Knights, are put in diplomatic services or the Agricultural Corps, helping with science and political duties with the benefits of their extensive Jedi education. (Perhaps Palpatine is one of these Jedi who were never chosen? His Force capabilities are thus known to the Council, and that is why he is not suspected when he's on the same ship or in the same office with them?)
9) The Republic fell because of corporate greed and interest group politics that caused for stalemates in critical votes when systems like Naboo needed the results of fast action. Imagine the California fire response if Republicans and Democrats argued the point of sending out-of-state aid until every house had burned down! Well, Naboo, and many of the Separatist Systems were on fire, so they had to take matters into their own hands. It is really surprising that Padme herself does not become a Separatist. I wonder if that will change? Right now, her position is to reform the Republic, because if the Separatists succeed, they'll only eventually need a new galactic government anyway, and learn soon enough that their non-interference policies will only go so far, before their precious commerce is destroyed. They'll need a New Republic, but out of desperation, carefully manipulated by the Sith, they'll help a war-weary population choose an Empire!
10) The Clone Wars were the clashes of an illegally, and unsanctioned Clone army, supposedly created by the Jedi, fighting against independent systems who were trying to create their own destiny because the corrupt or stalemated Republic no longer represented them, and they were lured by the money and show of strength by corporate interests, to trust that their automated droid armies could gaurantee their safety and freedom. The droids could not respond with compassion, and the feeling was almost bred out of the Clones, and what resulted was a war that escalated into the destruction of civilization.
11) Owen was the step-son of Anakin's mother, therefore Anakin's step-brother, and his son Luke's "step-uncle."
12) Bail Organa was a Loyalist Party member who believed in fixing the Republic and stood naively by Palpatine's side, as the Chancellor's ally, until it was too late. He helped the Chancellor gain emergency powers, which sanctioned the Clone Army, and then called upon the Jedi to serve as its generals. Obi-Wan was a Jedi who obeyed his call to duty. He served all the Loyalists to the Republic as a General, not just Bail Organa, but the two may yet end up fighting on the same side in action, or at the speaker's podium. It will be up to E3 to show us anything more.
The Questions left for E3 are as follows:
1) How does Padme die?
2) How does Leia end up with Bail Organa?
3) What makes Anakin finally choose to fight with Obi-Wan with weapons versus words? (he's already mad at Obi-Wan and the Jedi about his mom).
4)What physically happens to Anakin? What are his wounds?
5) How is Palpatine alligned with the Sith? Who was his master? What is he? How did he get into service in Naboo in the first place?
6) When are the droids' memories wiped? 3PO, or both? Why? (can't 3PO remember Tatooine?)
7) Where does Han Solo come from? Is his destiny intertwined in all this so early in his life?
8) What's Chewie's story? Where does his morals originate from?
9) When does the Rebel Alliance form? What will Bail Organa and Mon Mothma have to do with it? How about Admiral Ackbar (NOTE - Mon Calamari is Separatist! - Sen. Tiikes is in AOTC, and in the comics and in the upcoming CW cartoon, Mon Cal and Quarren alike fight Palpatine's Republic)
10) How does Tarkin rise to power? (it's not really important. He just has fans).
11) How is the Jedi Temple destroyed? Are all the Jedi killed, or are they still hunted for 18 years after the movie closes?
12) How does Yoda end up on Dagobah? How does Obi-Wan end up on Tatooine?
13) Does Vader know his son survived? Does Palpatine?
14) Did Anakin have a father? Did Shmi lie?
15) What ends up happening to C-3PO and R2-D2? Are they lost so they can have their "Droids" adventures for the next 18 years? Is R2 trying to loyally get back to Padme, or serve her daughter?
16) Does Obi-Wan meet Darth Vader, once Anakin is transformed?
17) Will Lucas keep Vader's identity secret, as to make for a 12 hour movie?
18) Will Lucas keep the fact that there are twin babies secret for the same reason?
19) Does Lando Calrissian have any significant origin in all of the calamity following the Clone Wars?
20) What has happened to Boba Fett?
21) How does Mace Windu die?
22) How do some Jedi disappear?
23) Do midichlorians have anything to do with any plot point whatsoever?
24) Did JarJar Binks serve any further purpose to the trilogy as a whole?
25) Why did Count Dooku get involved with the Sith? Why did Palpatine trust him? How did they meet?
These are a lot of the issues that have been, or have to be, resolved by the Prequels.