With a new Mac, even during "migration", the OS, System files, and Apple apps will always be "fresh" (the new copies on the new drive).
Old Apple apps don't get migrated.
Insofar as non-Apple apps go, if they were working "as intended" on the old Mac, I'd migrate them and see how well they work on the new one. If they -don't- work, then it's time to trash them and do a "new install".