One of Babylon 5's strongest points is the characters, the not so cliched characters. Unique and not transparent. The opinions we developed of them in the first season undoubtedly drastically changed by the end of the show. Nothing is what it seems, as G'Kar often said, making every plot twist that much more unexpected.
And the not so cliched bad guys. They werent just 'evil' for no apparent reason. They had reasons, and they all thought they were doing the right thing, making them so much more difficult to overcome.
The mystery in season 2 and 3 is exhilarating, and the way the show only gave us clues for the first two years. Everything just built up. The show started slow, like a regular episodic sci-fi at first, entertaining, but no big deal. But then conspiracies began to unravel, tension built until it felt like it was going to explode! and it did.
I would say it is a space opera, but perhaps with fewer cliched elements than usual, and somewhat more plausible.