voztimbrada: Thanks to you as well for the very nice response.
As for some examples... the first one that stands out the most would be the role of anti-semitism. Anti-semitism played a role in the yellow journalism printed about Frank which did bias people's views towards him, and Watson was for sure an anti-semite (though he didn't get involved until later) but as for the trial itself, it didn't have much influence. There was no shouting or out of controlness inside (Mary Phagan Kean loves to point this out) and several people in the jury were Jewish. I'm sure that being Jewish alienated Leo from people, but it wasn't like "Hang the Jew!" In fact, the claims of anti-semitism just further alienated the southerners, who were like "What, just because he's Jewish he shouldn't be punished for committing murder?"
Another big one are the characters and relationship of Leo and Lucille. They're really exaggerated: Leo is shown as this uptight, cold, Jewish Yankee who hates the south and feels that he is surrounded by hicks. On the contrast, Lucille is shown as this southern belle who's completely assimilated into the southern culture and forgotten her Jewish heritage. Parade did this for the sake of character development, which is fine, but in real life Leo didn't hate the south (he was born in Texas, for heaven's sake); he may have felt uncomfortable there, but it wasn't to the extent of what he sings in "How Can I Call This Home?" And Lucille was still immersed in her Jewish background. In Parade for example she asks Leo why he's using a Hebrew (or is it Yiddish? Whatever it is) word, when in real life she often used them herself. And their relationship is shown as very cold and distant until the ordeal brings them together, when actually they were quite close and happy in real life. Steve Oney actually had excerpts from their letters to each other in his book, and he concludes that they were quite in love. Supposedly at one point Lucille was even pregnant, but miscarried. I scanned Steve Oney's section on their relationship if you're really curious (he's the only one who's written in detail about it.)
Another big thing is the trial itself. The musical seems to focus more on the attacks on Frank for "sexual perversion": with the exception of Epps and Conley, it leaves out physical evidence (both for and against Frank) and witnesses who both accounted for Frank's whereabouts during the murder, and challenged it. For example, the biggest witness against Frank aside Conley was Monteen Stover, who claimed that he wasn't in his office at the time he claimed. The "murder notes" (two notes discovered next to Mary's body and allegedly written by her murderer; Conley admitted that he wrote them, but claimed that Frank had dictated them) are an especially large omission.
Some other minor things:
- Conley came up with his affadavit not because he was a runaway convict, but because he was an actual suspect for the murder himself
- According to Conley, Frank gave him $200 not $100 (sorry, for some reason that bothers me XD)
- Lucille did not get Slaton to commute the sentence, and most of Slaton's reasons for the commutation were changed
- Also, according to her mother Mary rather disliked George (Frankie in the musical) Epps; though the boy's father claimed otherwise
- Leo's behavior in jail in the musical also sticks out to me; he acts pretty snotty. In real life he was calm and thought he'd be out of there soon enough. Again, it's all for the sake of character development though...
- Lucille did leave Atlanta for a bit after the lynching
- This is unrelated to the case, but it drives me nuts all the same: the USA did not enter World War I in 1915! I am going to assume that Frankie Epps is going to go volunteer in Europe like Hemingway did.
These are a few examples... I wrote up an entire list on a webpage, actually, though most are just plain nitpicky.

If you have any further questions or comments, feel free to respond... I love to discuss this infamous court case. I don't know why it fascinates me so much, but it does!
Jimmy, what are you doing here in the middle of the night? It's almost 9 PM!