Another idea: since the main plot of A new threat deals with the Malevolence, I believe the Malevolence first scene should be placed right after the opening crawl (which would then need to be changed), à la A New Hope opening (action scene instead of a talkative one).

Opening crawl

First paragraph, the same

In a bold move, the Clone Army has won a striking victory on the planet Rhodia, by capturing the Viceroy of the TRADE FEDERATION, Nute Gunray.

Chancelor Palpatine has dispatched Jedi Master Luminara and Padawan Ahsoka (etc.)

Little does the REPUBLIC know that to stop its forces to advance further, the SEPARATIST ALLIANCE has built a new weapon, the MALEVOLENCE, a warship with the ability to annihilate entire fleets, which is reaching nearly completion under the lead of General Grievous and Comt Dooku….

First Malevolence attack
Ahsoka, Gunray, Luminara
Dug homeworld scene
Back to Gunray
Back to Dug homeworld: Palpatine sends Windu and Anakin on a mission to find the weapon
Maybe another Malevolent attack if there is enough material; or else you can directly show the two Jedi arriving to the Cruiser.

What do you think?