I think we shouldn’t cut after Qui-Gon’s death, this plotline is problematic because it has two consecutive low points, but if we go from Qui-Gon’s death directly to Obi-Wan falling in the pit, we end up with one big low point that we can pair up with Anakin stranding inside the control ship and Padmé being captured.
It also adds a bit of dramatic effect, because had Qui-Gon lasted only for a few seconds longer, Obi-Wan would have joined him against Maul. With this order we can also place Obi-Wan bisecting Maul before the destruction of the control ship and Gunray’s capture, thus placing the moment of triumph last, followed by Obi-Wan attending to Qui-Gon.
However we would lose Anakin restoring hope through his destruction of the control ship, in its place we would gain a cool cut connecting the scenes stylistically, if we go from Obi-Wan killing Maul with a green saber to the green lights in Anakin’s cockpit replacing the red.
All in all it should play out like this:
1.-10. the same as Eddie proposed, that works really nicely, I think
11. Continue the Lightsaber fight into the force field room (maybe the most jarring cut, because the fight essentially jumps from one level to another with only a short establishing shot between them)
12. Anakin joins the space battle (same as Eddies point 11)
13. Lightsaber fight continues, Qui-Gon is killed, Obi-Wan screams and just as Maul turns around to face him, the force field opens. Obi-Wan fights aggressively, but is thrown down into the pit by Maul.
14. Padmé and her team are captured and brought before Gunray (I think we would need another shot bridging the two scenes)
15. Anakin enters the droid control ship but is stranded
16. Maul taunts Obi-Wan, the later grabs Qui-Gon’s saber through the force, jumps out of the pit and bisects his opponent
17. Anakin restarts his ship and destroys the control ship
18. The Gungans are freed and we see how the droid army collapses.
19. Add a shot or two of collapsing droids to the throneroom scene, the Naboo pick up their weapons and the Viceroy is captured. Our heroes were victorious,
20. but Qui-Gon fell in the struggle, Obi-Wan knees besides his dying Master and promises to train Anakin.