There were some absolutely great players in Jordan's era. Shaquille O'Neal and David Robinson rank in the top-5 PER of all-time.
Charles Barkley is ranked 11th. Malone 15th. Olajuwon 16th. I don't buy today's players are superior to Jordan's era at all. It's just the game has changed, and its more perimeter oriented. Sure, I think today's perimeter players are better. But Jordan played in an era where big men were still truly dominant.
The big men in Jordan's era is much better by a large margin. And don't forget, Jordan played in the 80s. It wasn't just the 90s. He played in the era of Kareem, Magic, Bird, Erving, etc... Even a younger Kobe Bryant in the late 90s. Penny Hardaway and Grant Hill were superstars until injuries sidelined them. So he's gone against a vast variety of great players from different eras.