If i was going to play DH again, I would happily rewrite about half the rules. Some examples that came up in our game:
Overwatch (action, p223) - Allows you to fire at EACH AND EVERY target that meets the conditions you set. So its possible you can attack a dozen or more times in a turn.
Psychic Powers having no minimum PR score to use, meaning that undercasting is vastly superior for most uses.
Influence and Requisition of Equipment - according to p269 you could sacrifce 1d5 influence to automatically succeed at an influence roll unless the GM deems it impossible. So… You could requisition basically any piece of equipment and just have it. I don’t see any narrative reason to forbid most items when the PC’s are at a place where Imperial rule is strong - such as a planet with a naval base, inquistorial vessel in orbit, Planetary Guard armoury or so on. If the group works optimally, only one person would have any Influence after the first time they get to any such place, the rest spending it to tool up with power armour, relic force weapons, melta guns and so on.
The Snare quality - good god almighty, where do i begin with this. The rule itself isnt awful, apart from Immobilisation preventing you from using psychic powers or other mental/social actions. Its how badly implemented it is. A webber has snare 1, so a -10 penalty to avoid being snared. Ok. A Mancatcher (enemies within, p 46) has 4 so a -40, regardless of where you are struck by it.
There are others, but these are the ones I remember.
As to why the missions are badly written:
First, a beginner GM may have problems with the plots and structuring. They are written assuming that the group will do this, then this, then that, OR that they are happy to have the GM lead them around, OR that they can only visit places once they get clues about them.
Second, they are very unclear about linking scenes, clues and information that the characters can receive from various sources. As an example in Dark Pursuits, the adventure in the corebook, it is mentioned in the opening text that there have been several horrible deaths involving the archeotech, but none of them are detailed. Also the opening scene is very bare bones until the group get to Hesentanz manor by speaking to some nobles and making a test - which if failed gives the group no information. So many scenes rely on passing tests to get information or having information that the group has little or no chance to have acquired.
Thirdly, the encounter scaling is awful. The rules for designing encounters are ignored (which is fine, but you would expect the pre-written stuff to follow them to some degree), and encounters seem to be either far too easy or very difficult. We stopped after playing through Desolation of the Dead from the GM’s Kitbook, where the final encounter includes something that would have one shot each of the characters. The group only won due to a poor psychic phenomena roll on my part. Otherwise it was going to be a TPK, no doubt.
Lastly, the statblocks for NPC’s are just bad. They don’t include full skill listings for no reason, people are missing skills and talents that they probably should have (eg: fighting type characters having acrobatics instead of dodge [Vornas for example has neither dodge or parry]), some NPC’s have talents that don’t exist, or traits that they maybe shouldn’t (the boss in Desolation of the Dead has Touched by Fate, giving him 2 fate points making him basically immune to death, but the group are meant to be able to kill him and get bonus xp for doing so)
I think that all of these could have been solved by being proofread and edited properly, which suggests that they were probably rushed and that there was very little oversight from a developer. The expansion books - enemies within, without, beyond - suffer greatly from the writers seemingly not understanding the games rules and mechanics.
YMMV though. I think the underlying system is fine and some of it was even suprisingly elegant (character creation and development for example), but everything draped on it to make Dark Heresy 2E didnt fit well enough.