Now that it has been a few years since the game came out, and RT2.0 is probably coming in the next year or two, as a player or GM, which prewritten adventures have enjoyed GMing or playing the most?

Frozen Storm (From the GM Kit)

Intro 1: Into the Maw (From the Core book)

Intro 2 : Forsaken Bounty (pdf only)

Intro 3: Dark Frontier (pdf only)
Lure of the Expanse

Shedding Light (pdf only)

Soul Reaver

Twilight Crusade (pdf only)

Vaults of the Forgotten (Edge of the Abyss)
Warpstorm I: Frozen Reaches
Warpstorm II: Citadel of Skulls
Warpstorm III: Fallen Suns

Also, two older topics:

https://community.fantasyflightgames.com/index.php?/topic/48409-pre-written-adventures/

https://community.fantasyflightgames.com/index.php?/topic/62761-best-rogue-trader-adventure/

Personally, I like Frozen Storm the most. It needs a hell of a lot of build out and customization to your party to make it a really good game, but it provides one of the best lasting marks on the game and an almost endless set of adventure hooks.

You mean the Frozen Reaches?

I had good success with Lure of the Expanse.

Personally I tend to use the written adventures as a frame work to build a game on, adjusting or recreating as necessary for my group.

No the Svard/GM kit adventure. Frozen Reaches is good as well, particularly in how it handles ground combat, but like all of them can need some serious adjustment. Like I had to triple all of the orks. It's also one of those funny adventures that you can do in 3 sessions or 15, depending on your groups tolerance and how many sub-adventures/flashpoints/etc you put into it.

Actually I and my players really liked that adventure too. We just finished it a month or so ago.

They did things a little out of order and nearly lost installation 23, but managed to secure the fixer-upper system.

The final battle was great. They had 6 system ships, the cruiser, and their tricked out sword. The enemy had a half dozen system ships, one system ship converted as a fire ship, three void wasps, installation 23, and later on the Whisperer. We wound up setting aside their system ships and an equal number of enemy system ships and rolling it as opposed command checks the same way I do mass battles with mooks in the background while the players do stuff.

I described the Whisperer coming out of the cloud of interstellar stuff, but it was when I slapped down a black circle nearly a foot across on the battle map that they panicked a little. They wound up flying inside the whisperer for a bit, used up both of their carefully horded nukes, one of which they'd actually started the game with. The second smaller one they waited a round or two to fire off, but when they didn't seem to be getting anywhere they used it and wound up rolling silly damage, dealing far more than required to finish off the Whisperer, which wound up having a "warp drive"-esque explosion and nearly destroying installation 23, which they'd landed the Carrion Commandoes on in order to disable the installation's lance weaponry so they could conduct their fight nearby without having to worry about getting lanced.

Fun times.

What I think the great part about it is that it gives the players a number of ins, and something to care about in the expanse.

===Spoilers===

For example, I put the system just a bit off from Damaris (with Damaris it's primary trade link) so when Frozen Reaches came around, they had a personal stake - Stop the orks at Damaris or Svard will inevitably be next. In addition Keel gives you a potential link to the Navy, his brother a potential link to the inquisition, and Silence could have hundreds of years of family records and who knows what other documents. Plus, I made Installation 23 one of only a small handful of plasma-grade promethium refineries in the expanse, providing a unique form of leverage for negotiations. It's just chock full of opportunity. If I were to run another Rogue Trader game, Svard is probably where I'd start.

Linking stuff together like that is great. During the Lure of the Expanse my players made friends with Jeremiah Blitz, who luckily shows up in Frozen Reaches. They also royally (perhaps unnecessarily cruelly) screwed over Feckward, and he's now turned to chaos and waging a sort of cold war against them, having put out a bounty on their officers and crew as well as other stuff I won't mention. I also made it so Keel and his cousin (brother) were both Harlocks and had Inquisitional connections stemming back to the fall of the Harlock Dynasty (the story of which I'm mostly making up myself). So they'd both be making future appearances.

My party really wanted installation 23 extra bad because they're setting up a salvage operation on Dross after the Eldar device was deactivated (the ship graveyard plant from Lure of the Expanse). Having a large and ready supply of promethium, both for use and for sale, would be an incredible boon. Between the output of Cog, Installation 23, the salvage on Dross (actually renamed Char), it might make sense to set up a full shipyard over Char for a one stop ship/shop.

Side note, we seem to be going through the same AP progression. I did Lure, then Whisperers on the storm, and was setting up for Frozen Reaches before the game went on hiatus. If you ever decide to run an online play by post style game, consider the Myth-weavers or RPGCrossing sites and I'd be happy to join (you sound like a good GM). Rogue Trader as a player rather than a GM would be a nice change.

I really enjoyed playing Lure of the Expanse. I'm looking forward to finally running it in the near future.