We need to distinguish between 2 different occassions:

1. Original plot by Zam Wesell

   This was ultimately orchestrated by Sidious (via Dooku via Jango Fett).

   The goal was, as @Richard's comment noted, to remove a person opposing the Civil War, which was Palpatine's goal. Had Padme have her way, no G.A.R, thus no Order 66.

2. Sentencing Padme to death on Geonosis.

   First of all, the benefit is making sure she would not tell the Republic about a hidden Separatist operation there.

   If you recall from AotC, that place held plans to Death Star, among other things.

   Second, personal grudges by Separatist leaders (Gunray over Trade Federation fiasco at Naboo)

We need to distinguish between 2 different occassions:

1. Original plot by Zam Wesell

   This was ultimately orchestrated by Sidious (via Dooku via Jango Fett).

   The goal was, as @Richard's comment noted, to remove a person opposing the Civil War, which was Palpatine's goal. Had Padme have her way, no G.A.R, thus no Order 66.

2. Sentencing Padme to death on Geonosis.

   First of all, the benefit is making sure she would not tell the Republic about a hidden Separatist operation there to build droid armies.

   If you recall from AotC, that place held plans to Death Star, among other things.

   Second, personal grudges by Separatist leaders (Gunray over Trade Federation fiasco at Naboo)