Pros:
The Acquisition check system is brilliant. Instead of counting thrones, you just find a reasonable market and make a roll. Modified by the quality, availability and relative quantity of what you want, this system covers everything from buying a nice pistol to buying an army of mercenaries with their CnC materials.
The setting is epic in scope. Despite the fact that the Imperium of Man is a baroque, alien and bizarre place, the writers have actually managed to make the unexplored places of the galaxy even more alien and strange. There are a lot of thinly veiled references to H.P. Lovecraft (which is the only way I can imagine to make the Imperium seem banal) and you can reasonably expect to be traveling through "cyclopean ruins" fairly early on in the game.
Cons:
I hate the character creation system. I hated the random system in Dark Heresy, and I hate the "origin path" system in this game. Designed to produce a character that has a "reasonable" background, the results are too archetypal to fit into a game moved along by exceptional and unusual people. Luckily, you can ignore this system with no penalty.
I dislike the amount of charts in the game. Some of them, especially the Perils of the Warp, or the Critical Hits, are integral to the game. This would not be so bad if they were reprinted at the back of the book, as is done with most games that rely on charts, but they aren't.
Finally, I am not pleased with the paucity of NPC's in the back of the book. The Dark Heresy rulebook had 30 pages on NPCs, covering everything from daemon hosts to arbites. Rogue Trader only has 14 pages for this material, and much of it is redundant flavor text from other chapters.
Overall:
3.5 stars (and then just slightly more 'cause I'm a fanboy). Great game. The solid mechanics and great setting will provide many hours of fun. It is a bit annoying to prepare to run, though, and one would think that the high price tag would not require more purchases to clear these annoyances.