Here's why MJ would have won the series:
1. Jordan was a far better penetrator than Bryant. No team ever kept Jordan out of the lane. He was quicker and more athletic than Bryant, and was a stronger finisher. He was strong enough so that Pierce could never keep him in check one on one by playing physical defense... and if Rodman, Mahorn, and Laimbeer couldn't keep Jordan from finishing at the rim, don't tell me Garnett, Perkins, and Powe would.
2. Jordan was a far better defensive player than Bryant. You could stick him on Pierce, unlike Bryant. Kobe Bryant is the most overrated defender I've ever seen. He always plays the other team's worst offensive player (ie, Bowen, Rondo). First team All-Defense my ass. So anyways, Radmanovic wouldn't be guarding Pierce; someone with the strength to play physical defense while having the quickness to stay in front of Pierce would be.
3. Jordan could score on the block. You could always run a high percentage play for him on the baseline to make double teaming him difficult. An absolute go-to play that Bryant hasn't even tried to have in his arsenal since '04. What was the Lakers goto crunch-time play? Throw it to Kobe and have him shoot a wild off balance jumper?