Naboo is now Alderaan. At this point in time, Alderaan is the ruling planet of an independent system which has petitioned for Republic membership but is not yet part of that body.
The Trade Federation is now the Federation Neimoidia. Instead of being a shipping/trading conglomerate (or whatever), the Federation’s a compact empire of mercenaries which hires its services out to planets/systems embroiled in small-scale conflicts.
Qui-Gon remains Obi-Wan’s master.
Qui-Gon and Obi-Wan wear black uniforms, the standard garb of Jedi.
Qui-Gon is the Jedi watchman of the Alderaan system. As such, he and Obi-Wan are already present on the planet’s surface when the Federation invades.
Amidala and Padmé are now separate characters. Amidala is a child queen, 9 years old, innocent and demure. Padmé is one of her bodyguards, 17 years old, stern, with a lean muscular build.
Threepio is one of Amidala’s servitors.
Palpatine never appears in his Darth Sidious persona. It is Darth Maul alone who conspires with the Neimoidians. He is a human with red-&-black body tattoos, pristine white teeth, and a crown of feathers sewn with razor wire about his head. He wears white robes, the standard garb of Sith.
The B1 battle droids are replaced with BX commando droids. These droids rarely speak.
Qui-Gon, a nonconformist who straddles the line between orthodoxy/unorthdoxy, is the only Jedi who wields a green lightsaber. Obi-Wan, more by-the-book than his master, wields a standard blue Jedi lightsaber.
Gungans are present in the story, but Jar Jar is jettisoned.
Obi-Wan accompanies Qui-Gon and Padmé into Mos Espa.
Anakin is 12 years old.
Cliegg Lars assumes Watto’s role. Owen is Anakin’s only friend. It is implied Cliegg is Anakin’s father (and Owen his half-brother).
Obi-Wan’s explanation of the Force in SW '77 is transferred here and given to Qui-Gon.
No podrace. Qui-Gon successfully barters for Anakin’s freedom but hasn’t enough to buy Shmi’s.
Rather than a double-bladed lightsaber, Darth Maul wields a lightsaber pike. The shaft is of lightsaber-resistant metal, sporting a single red blade.
The Neimoidians erect planetary shield generators across the face of Alderaan. These generators, kilometres across in size, ravage the natural landscape and claim thousands-to-millions of lives.
There is no Chosen One prophecy. Anakin’s raw prowess with the Force is impetus enough for Qui-Gon to bring him before the Jedi Council.
The dissonance between Qui-Gon and the Council is greater here, with visible animosity between Qui-Gon and Mace Windu.
The Republic has a navy, modest but sizable enough to displace the Neimoidian presence on Alderaan. Being a non-member system, however, bureaucratic red tape prevents the Senate from assisting Alderaan. This is what inspires the non-confidence vote which ousts Valorum from the chancellorship.
Anakin remains behind at the Jedi Temple as Qui-Gon and the others return to Alderaan.
Allying with the Gungans, the Jedi & co. go to capture and disable the main shield generator. This is where Qui-Gon and Obi-Wan face Maul. Maul fatally wounds Qui-Gon and bests Obi-Wan. Rather than slay Obi-Wan, Maul considers the apprentice too unworthy to die by his hand and so makes his departure.
The planetary shield nullified, the Republic fleet arrives to beat off the Federation.
The ending mostly plays out the same as in Lucas’ film.