The constant running back and forth to the ship was a bit boring due to the 'tram whizzing along' cut scene and the lifts required to the stations- it felt like unecessary padding, but only a few minutes worth.
The battles with the enforcers- watching the enemy escape when you've beaten them again and again was a bit annoying. Some of them could have died just for a bit of variety, rather than running away because they can't be bothered to stick around any more. It's such an annoying thing when enemies get trounced, and then your characters, despite having an array of ranged abilities, watch them monologue and then flee, or instantly forgive their freely-chosen murderous ways. The lack of wanting to let many of the supporting cast of enemies get some kind of comeuppance (or at least be arrested/KO'd) despite them throwing their lot in with a cult that is happy to watch people die just smacks of 'our enemies are too cool for your victory to mean anything!' I wonder if the actions of the enemy foot troops will be as freely forgiven and forgotten as their leaders?
Having said that, anything from murder to treachery or attempting to overthrow the ruling power to firing up ancient weapons of mass destruction all seem to be crimes of very minor consequence in Liberl as long as you have a very personal, unresolved reason to do it.