I’d say Bounty should be kept in. It’s the episode which introduces Ventress to bounty-hunting and also serves as context for why is she on Tatooine competing with other hunters for the prize on Savage (in Revenge), and later on Coruscant willing to capture Ahsoka in exchange for payment (in the fugitive Ahsoka arc). Besides, the train action scene is pretty fun and sometimes even brutal.
Both Massacre and Bounty could be moved up a few episodes as long as they come after Deception. In Massacre in particular, with its current place in the timeline, doesn’t make much sense why Ventress takes so long to get back to Dathomir or why Dooku takes so long to get revenge on the witches.