I did both, not much of a difference.
I upgraded my mid-2010 iMac and that's the way it's running now.
I first upgraded my mid-2009 MBP and then, because my MBP is my "playground" and "testbed" I did a fresh install a couple of different times with and without using migration assistant, using different combos of migrating user data and applications. I finally settled on not using MA at all and reinstalling all my purchased apps.
I have iLife '11, MS Office '11, PS 5, LR 3, Handbrake and free XCode as my big, "important" apps. I have about 26G of music, 40G of photos and about 300G of transcoded DVDs and other home videos.
I didn't collect any careful analytics, but I can't say I noticed any differences (speed, temperature or whatever) with any of these methods.