Rogue Trader has to be one of the most interesting and innovative table top RPGs I've come across in a while.
The game mechanics for the system itself are not really that revolutionary. It's a straight up percentile system - something - fans of Call of Cthulhu should be familiar with. If you ever played the old RPG Inquisitor by Games Workshop, much of the Rogue Trader's system will be familiar.
However, what makes Rogue Trader so innovative for me are the various ways the designers approached campaign design and structure.
First of all, let me say that Rogue Trader is very different from many other table top RPGs in its very premise. In many pen & paper RPGs, you begin with the premise that you are nobody, or at least lower-level operatives in the world at large. However, through time, effort, story, and perhaps some experience points, you can rise to become a potent force in your character's environment.
Rogue Trader does away with that and presumes that the characters you play are already powerful individuals with long and turbulent histories. In this game, you are the members about a Rogue Trader ship, a vessel of grand size and vast power. You begin the game commanding large forces and troops. It's certainly a different approach to table top roleplaying than what I'm used to.
Characters for Rogue Trader start with a lot of experience under their belt, and their backgrounds are determined on a large flowchart. The flowchart allows the players to find commonalities between their characters, possibly sharing backgrounds. Perhaps your player character and the guy next to you fought on upon the death world of Woe. Or perhaps you both served on the same freighter.
What is really interesting about this for me is that in ye olden days, all of that was determined by you and the players. The player characters may have know each other at the start of a campaign. Or perhaps they just met at a tavern. More importantly, there was very little in the way of aid for the Game Master or his players when it came to establishing relationships and commonalities between the different characters. You were just supposed to know how to do this and do it well.
When you go it alone, much of what happens is trial and error. In my past, I think a lot of table top gamers can relate to experiences in which a party or campaign collapses because the characters made for the game don't mesh. Or perhaps the characters are trying to go off and pursue their own agendas.
Rogue Trader is one of the few games I've ever seen where the implied rule is that everyone sits down and makes their characters together. I've seen RPGs encourage this, but the implication in Rogue Trader is that this is almost necessary.
Besides that, there is also an implied system for campaign creation and plot. The Rogue Trader game has a number of tools which allow players to drive the story, not the GM. While plenty of people prefer games where the player characters drive the story, again, it's always been the GMs job to set up a system to let this happen.
In Rogue Trader, however, this is a system of Endevours, which are small, self contained story arcs. The GM is expected to create Endevours for the PCs to tackle, assigning them point values, and creating objectives. Each objective should bring a rogue trader party closer to completing the Endevour.
While this may seem a bit video-gamey to some, I love it. It means that, at the start, I can lay out on a map what missions there are out there and what it may take to complete each one. But also, it's implied that the players themselves might be able to suggest their own Endevours, at which time the entire table might hash out the objectives through discussion and consensus.