Yes, you can choose which apps and files you want to migrate. It is quite straightforward and easy to use.Could someone please clarify: does Migration Assistant let you choose WHICH applications, or is it only set up to take ALL of them? If the latter, it might behoove me to clear out ones that I don't want to migrate on the old system first. If the former, it doesn't matter.
You believe wrong.....I believe Migration Assistant (and Setup Assistant) will "migrate over" -ALL- your applications. You can't pick-and-choose them.
The "basic Apple apps" (such as Safari) won't be migrated, because the newer version will already be on the new Mac.
When there are newer versions of applications, the older version is not migrated, but content and settings are. You can select what you don't want to migrate.