Migration is still a fresh OS install. When you have hundreds of apps (I have some going back all the way to 2001. 1986 and OS 3.2, if you count the Mac Plus emulator), reinstalling them becomes cumbersome, to say the least. Migrate first, then if you have an issue with an app, you can always reinstall (or delete the prefs, app support, and app manualy, and reinstall). I usually still need to reenter some serial numbers, but it's still much faster than reinstalls.
OP - you have to do what you feel is the best for you, though. If you only have iLife and a couple of the major apps (Office, Adobe CS), then the difference in effort is less significant.