Has anyone mentioned "Legend of the Galactic Heroes" yet?
That's a really good series. Don't let the dated visuals or the sci-fi setting fool you either, you come this show for the characters and the storyline.
It all basically centers around an age old conflict between the Galactic Imperium (mainly focussed on the Admiral Lohengramm), and the Republic (main character here is Admiral Yang-Wenli). A lot of it is about the conflict between the ideals of democracy and authoritarianism, and how the characters view this as they pass through the conflict. There's a lot of philosophising on both sides of the conflict as to what precisely they're fighting for, and none of the main cast are pegged as outright "bad guys" (and there is a pretty huge cast over the course of this show). Everyone has a reason for their actions.
It's spread out over 100 episodes, so it'll give you plenty to work through too. And unlike most long shows there's very little if any filler, there's always something significant going on, with events that happen early and mid-way through the series still having their effects throughout. It didn't appear that they were afraid to take risks with either the story or the characters, you can tell it was based off of a series of novels.
Space Opera is rarely done like this anymore, and even more rarely is it this well executed. Sure the space battles never made too much sense to me (I'm pretty sure that they were winging a lot of that stuff), but I can live with that for a show that makes an effort to become something more wide-ranging and epic.