The final arc in general was quite... questionable, but I see it as no different than later episodes of Teenage Mutant Ninja Turtles, or any such thing. I would still stand by the comment that it tried more than other mentioned shows did. I mean, the ending to JLU was pretty much a slap in the face with the Justice League letting the Legion of Doom go.
Indeed, she was, though I'd argue that's an example of sexism than anything that has to do with the nature of serial storytelling, especially when there's quite a few counter examples.
I don't like superhero comics for that very reason, actually. No real endings, loads of retcons and other similar things. ( I read them for awhile, but quickly grew tired of them for those reasons.) Movies are a bit of a different thing, as most of them tend to kill off the main villain and offer some semblance of closure. So I'd rank them better than the comics, at least. However, all those movies are live-action rather than animated (though recent years has lead to some DTV for Marvel and DC properties.)
I view it as nothing more than another episode, myself. It tells us nothing we didn't already know, and felt more like a shout-out to the comic story it was based on rather than anything else, especially when it's never really mentioned again. If it was referenced or important later on, then that would be something different. Even if we do agree that it's important and worth telling, then there's still ways to incorporate it into a main story (it could have been a ploy of Cadmus instead of Mongul, for example).
Could you list them? Provided we're on the same page of cartoon series with an actual story that has an actual ending. A lot of shows may technically have a goal (Samurai Jack and Megas XLR, to name some recent ones) but only use it as an excuse to air as many self-contained stories as they can until cancellation. A few seem to try to tell a story, but end up getting canceled on a cliffhanger and possess no ending (such as Exosquad and Pirates of Dark Water) American animation seems to get the short end of the stick in that regard it seems.
I also once liked the 80s Ninja Turtles series. I never claimed to be perfect. Tastes change, mature, and (hopefully) improve with time. It's just also preferable that animation improves along with them. As of now, it feels like not many American animators here treat animation as a serious medium for storytelling (or at least, not in the same way Japan has proven it to be capable of) Or perhaps there's people who do and the executives are the ones to blame. Regardless, they're not being made, which is extremely unfortunate.