It’s not being portrayed as a villain, it’s being insulted which happened during the Last Dance.
I think Isaiah took exception to the whole “we didn’t shake hands” debacle when he explained thats not how it was done back then Jordan kind of threw him under the bus. I think that was a situation where they both were “right” in a sense.
Isaiah later on made a great point that when they beat the Celtics, they didn’t shake hands either, Isaiah had to go approach Kevin Mchale as the Celtics were leaving the court to get a handshake and some words of encouragement.
Jordan’s point was that everytime the Pistons beat the Bulls HE and the team would shake hands so he wanted that same courtesy when the tables were reversed. Jordan wanted that moment as he felt he’d earned it.
At the end of the day I think the issues between Jordan and Isaiah are complex due to both being highly competitive. Jordan came to Isaiah’s city and pretty much took over and that couldn’t have sat well. Jordan never forgave Isaiah for allegedly leading a freeze out of him at the 85 All Star game when Jordan was a rookie. Plus all the Eastern Conference battles they had, “The Jordan Rules”, and the fact that the Pistons DID whoop his ass (physically). Problem is isaiah mostly left it on the court and always gave Jordan props publicly while Jordan took it all to heart. I think leaving Isaiah off the dream team should’ve made them “even” but we all know Jordan takes things personally that other athletes are able to get over.