Yeah, a show I liked named Gargoyles went through a similar art change in its last season as well. (That's another great show-I would highly recommend checking that series out!)
I hardly remember Batman: TAS' last season and it isn't shown much. HUB seems to favor episodes from the middle of the series' run.
"The Laughing Fish" and the one where Riddler puts Bats into a virtual reality game are shown often.

"I have an army!"
"We have a HULK!"
Loki and Tony Stark, The Avengers.