I'm currently moving data from an old MBP with FileVault on to a new MBP and it seems to be taking for ever, even using Thunderbolt. Does unencrypting/encrypting slow things down dramatically?
Typically the best practice here is to disable File Vault prior to migrating your data. Weird things can happen otherwise. It can take a little while longer to run the migration but I don't imagine it'd be terribly longer.