IMO, BSG was still awesome throughout most of the series, despite their fly-by-wire writing. Baltar is still one of my favorite characters, in all of his forms. Also, I think the Cylon navigators were one of the most inventive characters, and were fun to watch. (Jump.)
DS9 is good, and character development is one of their stronger points. Though, you can tell that they were initially going to just go with the same TNG episodic style, until they saw B5. MJZ practically invented story arc progression. I don't think I can recall a series before it that really dived into that mode. Nowadays, it's the norm, but Babylon 5 direction was the first and still the best way to write this stuff.
The only other series that I know of that really followed that model was Farscape. The writers knew their secrets prior to revealing them. But, it also showcases the pitfalls of proper planning: faith that the producer isn't gong to cut funding. The entire-season-condensed-into-four-hours movie showed all of the cool stuff they were going to do, and at least they got to show THE secret they had been holding through (which really put an exclamation point to a fantastic series), but I really wished they were able to produce that last season, like MJZ was able to do. (And then TNT fucked HIM over with Crusade.)
Firefly, Farscape, Babylon 5. Sci-Fi doesn't get any goddamn respect, and I fucking hate that.
Rosalina: But you didn't.
Robert: But I DON'T.
Rosalina: You sure that's right?
Robert: I was going to HAVE told you they'd come?
Rosalina: No.
Robert: The subjunctive?
Rosalina: That's not the subjunctive.
Robert: I don't think the syntax has been invented yet.
Rosalina: It would have had to have had been.
Robert: Had to have...had...been? That can't be right.