So my group just finished lure of the expanse and it was very enjoyable. The only question I have after the fact is has anyone played it with upgraded enemies? 90% of the enemies seemed to easy, meaning their guns literally had no chance of even causing 1 wound to one of the pcs, thats with starting armor for some of them. Some of the descriptions had said to add shotguns to mutants and things like that, but that literally didn't do anything as a shotgun with 0 penetration's damage will get eaten up by armor and toughtness real fast. Not that i'm going to run it again, but i am planning on running the warpstorm trilogy and want to know if its ok to make the enemies a bit more dangerous or should i leave them for some reason i can't see?

Also, on a different note, how often do you let your groups search for items they want? I've been letting them search for just about anything they want when they are on a station or planet, but it seems like thats quite a bit.

I ran into the same problem you did. Lure really is balanced for a new group to take on right away.

As far as acquisitions, in Into the Storm, there are additional rules that make it much better. The basic one that you're probably looking for is a cumulative -10 to multiple acquisitions in the same session. Aka first one as normal, second one with an additional -10, third -20 ect. It slows down acquisitions pretty quickly.

The easy encounters in Lure of the Expanse are there mostly for your group to get used to the combat system and start feeling like total badasses. That way, when you start adding xenos and powerful rogue traders to the mix, the contrast is huge and the effect of being in over their heads is increased. Remember that mood is about contrast.

I find that giving different kinds of ammunition to the mooks greatly increases their firepower. You could also try the horde rules from Deathwatch and Black crusade to up the ante. Flamers are also lethal and remember to take the environment into the ecuation, vats filled with toxic waste, perilous cliffs and narrow ledges. Grappling the pc's and ripping off their armor also works in a pinch.

I modified Lure of the Expanse wuite a bit. Added some Eldar aspect warriors here and there, upped the crew rating of all thebad guys ships, etc.

Victory is so much nicer when it was hard to achieve.

Of course you can make the enemies nastier and tougher or give them access to some nasty ammunition or guns. In my campaign, the use of armor isconsdiered to be more a thing of fashion then practicality since most weapons go right through it. For your campaign, I would suggest to updating the main encounter so that it will be a good challenge to the pc's. Let them wade through lesser mooks with impunity. Describing what happened at those lesser encounters instead of playing them out.

My personal pet peeve is that my PC's are very good. Most of their key skills are in the range of 90+, so unless things are very challenging they automatically succeed. The problem is that their opponents are not that good by far. A boarding action where one side has 90 and the other 40 is a done deal for example. They also got some nifty BS especially with some cyberware to integrate them with the weapon systems. Hence, the crewrating of their vessel is due to pc's doing their thing way way beyond the 30 of their crew.

I need a way to update their opponents likewise to make it a challenge.

Hellguns. Only d10+3 damage, but penetration 7 is good for getting attention. Or hotshot clips. Or the rules for setting a lasgun to a high power level.

Mix it up. Tactics, diversions, heck, set fire to something. Search for Tucker's Kobolds for ways that "level 1" foes can lay some hurt on PCs that individually outclass them.

Make the objectives more complex so that simply slaughtering everyone in their own time isn't a viable solution. Give them choices with consequences, but make sure you offer them (wherever reasonable) sufficient information to make a choice they understand. They can rescue the hostages but let the terrorist leadership escape, or take out the leadership at the cost of the hostages. A simultaneous assault increases the risk of unexpected complications that could mean one or both elements failing, or costing more resources than were planned.

Personally, I like to remind myself that balance in Rogue Trader is a waste of time. PCs have superior skills, equipment, a stack of Fate Points and oh yeah - a freakin' starship. Give them conundrums that can't be solved with firepower, moral choices, decisions that have consequences that affect them and the people that care about and rely upon. Just keep it interesting!

If you've got Deathwatch of Black Crusade you can always makes things a little interesting but throwing in a side-encounter away from the books in the form of a warband of Chaos Space Marines or a Tyranid Hive Ship. That should give them something to struggle with.