I definitely agree about the fact that there was more to explore with Terry, following the Return of the Joker storyline. Given that Bruce generally established the Animated Universe with his series, and was joined by Supes, he was the general mainstay. Batman was in every series, and to come to Batman Beyond, and have him replaced, it was fascinating to see what his place would be in this world, and how Terry would be accepted by the other heroes.
I particularly loved the efforts to establish a viable rogues gallery for Terry, rather than the easier method of using Bruce's villains without explaining how they could live so long and torment him (except, of course, the Joker. It was vital to bring back Bruce's greatest foe and put the new Batman to the test against him, and it was great to see Terry erase the Joker completely by proving he was as good as Bruce whilst being a different ballgame completely). I especially liked Blight, because it was effectively the creation of Terry's own Joe Chill. Inque was the best of the bunch, even if it was a little creepy with the odd sexual tension of some moments, and I don't remember his name, but the guy who could manipulate sound was fascinating, too, especially in his second appearance.