There probably could not have been a Michele Obama if there had not first been a Hilary Clinton. So while I like Michele, I think Hilary was the one who forged the way for the independent and educated woman. She wasn't liked at first for that, but gradually we understood that she was creating her own identity as a First Lady.
I believe Hilary Clinton made one of the best First Ladies the United States will ever see. During Bill Clinton's time in office she worked and helped draft a Universal Health Care bill that was probably far better than the Act we ended up implementing. She spent far more time and effort trying to do good for the people during her time. That's not to say that Michele Obama hasn't done well, Clinton just did more and often in the face of opposition.
If I had to pick one, it would be Hilary Clinton. Hilary had much more experience in assisting her husband in his government affairs. She was also somewhat vocal on many issues, including trying to get national health care on the table. She also seemed friendlier. Michele Obama seems less experienced and more cold and distant as a personality.
The first lady was not elected and therefore does not need to be political or politically active, but in practice, a politically active first lady is an asset. Michelle Obama is great, and seems like she's brilliant and just a cool person all around, but Hillary's political activity has her beat.
Michele Obama is slightly more preferable than Hilary Clinton. My primary reason for this argument is that Hilary Clinton always seemed to be persueing her own interests, her political career. On the other hand Michele Obama works on a variety of projects, and is always their to support her husband in his role.