This comes from www.starwars.com
Ben Burtt, editor, sound designer answers.
Why was Plo Koon and Ki-Adi-Mundi's commando raid on the Droid Control Ship cut from the final edit of Attack of the Clones?
The attack on the Droid Control Ship was filmed and edited together, but never completed with final special effects. A Jedi attack force battled its way up the ship's ramp, through doorways, down halls, and into the bridge of the ship. The scene was filled with much swordplay and stunts.
The sequence was dropped from the cut because it added another story to be intercut with what already was becoming too complicated and time consuming for the climax of the movie. Including the sequence also meant time needed to set it up and resolve it while the arena battle and the Clone War land battle proceeded simultaneously.
There was lots and lots of material in each one of these sequences that needed to be trimmed. There was lots of Jedi action in the arena fight dropped, more Jango and Mace, and even at one point a battle in space with the Droid Control Ships.
All of these would have been great to see, but choices have to be made for the priorities of the storyline.
Too bad he doesn't mention anything about the DVD cut scenes.