I find myself agreeing with the original poster. I'm new here and I've only played a dozen hours or so, so I doubt I've seen it all, yet the first time I played through I actually got bored of the murder mystery because nothing was happening, so I just decided to walk out one of the gates and got slaughtered by my first encounter.
For me it's an issue of pacing. The game starts fairly fast, with a nice early fight against crabs, then the orc encounter, a burning ship and you're right in the middle of your murder quest, the reason you are there in the first place. Then the game pace slows to a crawl.
I'm not sure that adding combat in the town is a good idea. But I think the pacing of the plot needs to be improved. Maybe interrupt the plot for something important, or even just stop the plot (waiting for someone to return for example) and "encourage" players to explore the other quests and get out of town.
If you do what I did my first time and focus on carrying out your orders then after those first two encounters there's not another fight for literally hours.