Clones Were Originally The Villains
Another problem with attempting to reconcile the Star Wars Legends stories with the modern canon is the status of clones in relation to the Clone Wars. Prior to the release of Attack of the Clones, it had been largely assumed that the clones were the villains and had been created to fight against the Old Republic. Attack of the Clones revealed that the opposite was true, and that the clone armies of Geonosis proved to be the Old Republic's salvation in the war with the Separatists. For all the complaints that the prequel trilogy inspired, most agreed that Lucas' conceit of turning the clones into the heroes of the Clone Wars was a brilliant twist, given that clones are typically the villains in most science-fiction.
This was the case in Heir to the Empire and the rest of the Thrawn Trilogy, which established much of what was believed about clones and the Clone Wars in the Expanded Universe for two decades. Most of these details were revealed through one of the chief villains of the Thrawn Trilogy, Joruus C'baoth. He was an insane clone of a fallen Jedi master, who sought to reestablish the Jedi Order with himself as Supreme Grand Master and all other Jedi as thralls to his will.
Through Joruus C'baoth, Zahn introduced the idea of clone madness - the conceit that if a clone was grown too quickly, it would be mentally unstable. It was originally unknown if this was due to rushing the process to create a clone (which was recommended to take 3-5 years) or due to the effect that copying an individual had upon The Force. It was later determined that it was indeed the influence of the Force that caused clone madness, as those clones created in a Force-free zone could be generated in 20 days with no mental or physical degeneration.
Clones of Force users, it seemed, would always develop clone madness, due to the problems the Force suffered in attempting to respond to what was essentially a single person existing in two places at once. Luke Skywalker confirmed this when he was forced to battle Luuke Skywalker - a clone Joruus C'baoth had created from Luke's severed hand and armed with his first lightsaber, both recovered from his battle with Darth Vader at Cloud City.
Virtually everything Zahn developed regarding how The Force perceived clones would be contradicted by The Clone Wars animated series. The idea of clone madness was abandoned outright and the idea that Jedi could not be effectively cloned was disproved by later stories. As for clones being viewed as the same person by the Force, Yoda told a Clone Trooper who despaired at lacking an individual identity that "In the Force, very different each one of you are" in "Ambush."
The Clone Wars Did Not Create The Empire
The largest and most impossible difference to reconcile between the prequel films and the Star Wars Legends material is the conceit that The Clone Wars helped to establish The Empire. Given that the earlier material was based around the idea that the Clone Wars ended 35 years before the events of A New Hope, there really is no way to justify those stories in the current timeline. There is not enough wiggle room within the canon established between the prequel films and the Clone Wars animated series to justify the better part of what was presented in the EU.
Ignoring the material written by Zahn which paved the way for most of the Star Wars Legends material, there are still other conflicts between the new history and the old. The first Illustrated Guide to the Star Wars Universe published in 1994 affirmed 35 BBY as the end of the Clone Wars - the same date Zahn had been given. The Farlander Papers - a novella released with the Limited Edition version of the 1993 X-Wing computer game - recalled the history of the galaxy, as told by Mon Mothma, who spoke of "decades of peace" between the end of the Clone Wars and the rise of the Empire. The greatest impossibility, however, lies in reconciling those stories which claimed that President Palpatine declared himself Emperor and exterminated the Jedi long after The Clone Wars were over.
Such justification at this point seems pointless, given that the vast majority of fans are quite satisfied with the history established by the Star Wars: The Clone Wars animated series. For the most part, these older stories are best regarded as a curiosity best pondered by those fans of a scholarly bend who like to examine what was and ponder what might have been. Thankfully, a new wave of novels is even now expanding the universe of Star Wars in the time between Return of the Jedi and The Force Awakens, reestablishing many of the classic characters of Star Wars Legends, if not every single bit of technical minutia. Given that Star Wars is, at its heart, a story of people rather than an examination of hard scientific ideas, this is likely for the best.