Bizarro Episode: "Transylvania, January 1918". It comes out of nowhere and even years later still makes no freakin' sense. (In the original, never aired cut, the Transylvania episode was told as a ghost story by the old Indy to some children in Halloween. So there was the possibility that it was completely made up. But then the new cut had to screw it completely...) It does, however, feel closer in tone to the movies which often have supernatural shenanigans and goings on.
Breakout Character: The older Flanery Indy proved to be much more popular than the younger Carrier Indy, to the point where most people know only his era of the series.
Fanon Discontinuity: Some fans of the movies prefer to ignore the TV series. However, the re-cut of the series (which does away with the frame story that causes most of the tension) has been better received.
Growing the Beard: The Sean Patrick Flanery episodes are able to be have more varied plots, greater stakes, and more character development than the Corey Carrier episodes. The Carrier era is also repetitive, since its plots largely revolve around Indy running off and having mild conflicts with his dad.