What a coincidence! I just beat it today as well.
[spoiler:ac35207746] It dissapoints me that even though they crammed as many Batman villians as they could, Joker is still the primary antagonist. Mark Hamill is great, but I'm getting sick of Joker. Is he really that great? He's just a lunatic dressed in a clown suit. An iconic lunatic in a clown suit, but still.
A great primary antagonist would be Two Face. This may seem a little biased since he's my favorite comic book character, but hear me out. Half of him is the man he once was. Harvey Dent. The other half is someone no better than any of the other major villians. The only way he can decide which side gets their way is through a coin flip. Plus, in Batman TAS, Bruce and Harvey were friends before the the incident. It shows how Bruce really wants to save him, but he still has to take him out like he would any other villian. [/spoiler:ac35207746]