I don't believe you can use Migration Assistant to "select" which apps to move, and which to leave behind -- it's "all or nothing".
Easiest way would be (as you said) to transfer them all and then delete what's not needed.
After doing this, you might want to also look in the "Application Support" folder (in your home library folder) and "root out" any additional files that may have been migrated.
If you REALLY want to "do it cleanly", perhaps the best way is to re-install all the 3rd-party apps you'll be using...