I've been playing more Rogue Trader lately and I'd like to share couple of thoughts how I see it in comparison to WoTR. Of course everything below is just my subjective opinion and anyone feel free to disagree.
First of all, Owlcat managed to improve lore presentation and overall writing since WoTR, which is already a big accomplishment, because both were really good in WoTR already. I always loved crpgs with massive walls of text, but I noticed, lately I often lack the patience to go through it. Yet, in Rogue Trader it's so well written and interesting, that I virtually read every bit of dialogue, infopoint or book. It 100% hit my sweet spot.
Secondly, not sure if it's by design, but Rogue Trader feels much smaller in scale than WotR, both from a world map and individual locations point of view. Exploration is not as engaging as in WoTR, because locations are usually small, with large rooms and very few secret or hidden spots (Persuassion checks are easy to pass). Also, even if there are quite a lot of star systems to explore, there are just a few worlds on each of them and only small fraction contain anything special (usually location to explore or dialogue-like event). Quite a rudimentary world exploration, which I actually like.
The more I play the more I like combat. Each level gives you something you can utilize in combat, expanding your set of options. My main gripe is encounter design. There are far too many mob enemies, that can be killed with one shot, and enemy placement is quite lazy. I dearly miss verticality, which adds a lot depth to combat encounters.
Overall, not sure if I can rate Rogue Trader higher than WoTR. Probably not, although I really appreciate smaller scale, because I find WoTR too big. It's a solid 8/10 to me so far.