The rulebook is absolutely atrocious. Absolute garbage formatting that forces you to look in 5 different places for anything.
Once you get a basic handle on the game though, it flows really well, especially for a more trenchcoat style with lots of background plot and mysteries to uncover. The lore is what keeps me coming back more than anything else though.
However, there's 3 aspects of the rules that I consider very crunchy and clunky, and I houserule:
Grenades in enclosed spaces. Nobody has time to sit there and do linear algebra to figure out how many times the shockwaves bounces between two walls doing damage each pass. If you throw a grenade into an enclosed space, chunky salsa and we move on with our lives.
Non-combat decking. If you need to hack the system while your party is being attacked by enemies, that's a cool combat encounter for everyone. If you want to get the floor plans of the building during legwork, I'm not having the decker run a solo session getting the data while everyone else stares at their phones. I make the decker roll a computers + logic test, give them info depending on successes, and we all move on.
Certain spells are absolutely horrendous in terms of how they affect the game. The 2 worst offenders are mob mind and chaos. Mob mind because you roll resistances for every single goddamn person in the area. I just make a very rough average of a nornal civvie, and houserule that the more excess successes you have the more people "failed" the save. Chaos has no written spell effect. I made my own table, with random effects ranging from fire to input failure to software glitch and lots of other possibilities. Keeps things fresh.
Jeez, that turned into way more of a wall of text than I intended, sorry.