Well, bottom line, going just by the results of the competitions and not our opinions and preferences, Michelle was the best skater in the world in the1995-96 season. And she was the best skater in the world in the 1999-2000 season. And in the 2000-2001 season. And in the 2002-2003 season.
Other years, other skaters won that honor.
I guess it depends how you look at it.
In the 95-96 season Kwan was the best skater in the world all season, and followed it up by winning Worlds so best skater that season is definitely Kwan. In the 96-97 Lipinski was the the best skater in the world during the period of U.S Nataionls/Europeans onward so best skater that year is definitely Lipinski. In the 97-98 season Kwan was the best skater in the world all season, except for the fact Lipinski won the biggest event of the whole season-the Olympics, tougher call here. In the 98-99 season Kwan was again the best skater in the world all season, except for the biggest event of all-Worlds, where Butyrskaya was clearly the best skater there, so again tough call. In the 99-2000 season Slutskaya was the best skater in the world most of the season, but not at that seasons biggest event the Worlds, so another tough call. In the 2000-2001 season Slutskaya was again the best skater throughout the season except for Worlds-that seasons biggest event, where again it was Kwan, another tough call.
In 2001-2002 Slutskaya was the best skater most of the season, but Hughes was at the biggest event-the Olympics. In 2002-2003 it was Kwan whenever she competed.
2003-2004 brings us the toughest one of all. Cohen was the best during the GP series where Kwan was mostly absent, but Suguri and Arakawa were both competiting(Arakawa losing to Cohen at 3 different events). At the GP final Suguri clearly was the best, and the rightful winner of the GP final over both Cohen and Arakawa, Kwan being absent. Kwan was the best at U.S Nationals over Cohen. Arakawa who had been solid and very strong all season, but not the best anywhere, was the best at Worlds, with Cohen and Kwan winning silver and bronze, and Suguri way back in 7th, so who was the best this season?
2004-2005 Slutskaya was the queen of this entire season I am proud to say, no doubt about it.

2005-2006 Slutskaya was the best during the GP series, with Asada and Arakawa both competiting, Cohen only doing 1 event. However Asada, the second best skater during the GP series, was the best skater over Slutskaya at the GP final, with Cohen absent. Arakawa after not even making the GP final despite being the 3rd or 4th best skater during the GP series(tough fields drawn too), and only being 3rd at her own Nationals, and not even going later to that seasons second biggest event-the Worlds, was the best skater during that seasons biggest event of all-the Olympics, winning gold over both Slutskaya and Arakawa, with Asada absent. With Arakawa, Slutskaya, and Asada all absent, Meissner ends up being the best skater at that seasons second biggest event-the Worlds, winning in decisive and clear fashion with Cohen in the field. So again which out of Arakawa, Slutskaya, Asada, or maybe Cohen was the best skater of this particular season.
This season Ando is the best skater during the GP series by a bit over Kim and Asada perhaps(1st and 2nd for Ando, 1st and 3rd for Kim, 1st and 3rd for Asada). Kim is the best skater during the GP final, Ando is clearly a better skater during this event then Ando though. Ando is the best skater during worlds by a bit over Asada overall.
So I see it:
1995-1996 season best skater-Kwan hands down
1996-1997 season best skater-Lipinski hands down
1997-1998 season best skater-Kwan probably, but an argument for Lipinski(OG)
1998-1999 season best skater-Butyrskaya probably, but an argument for Kwan
1999-2000 season best skater-Kwan probably, but an argument for Slutskaya
2000-2001 season best skater-Kwan probably, but an argument for Slutskaya
2001-2002 season best skater-Slutskaya probably, an argument for Hughes(OG)
2002-2003 season best skater-Kwan hands down
2003-2004 sesason best skater-Cohen probably, argument for Arakawa or Kwan
2004-2005 season best skater-Slutskaya hands down
2005-2006 season best skater-Arakawa I guess, even Asada, Slutskaya, Cohen?
2006-2007 season best skater-probably Ando, argument for Asada or Kim