The reputation system is based on witnesses best I can tell. It's a reputation system, not a moral compass. It doesn't represent character guilt, it represents public opinion. So yeah it makes sense that you can hack bank accounts with no penalty because nobody sees you do it. If you rob a store, people see that. If you run people over in a car, people see that. Luckily though, there is no major penalty for playing a bad guy. It's just likely people call the cops on you. Hilarious random event: sneaking past some guards, I hack a grenade, guard hurls it into the street before it explodes. It lands in a group of 4 civilians and kills them. Guess who got negative rep for that? So yeah, the witness thing doesn't always work.
I haven't played enough different games to know what people complain about driving wise. I played GTAV and it feels the about the same to me. Aside from the occasional physics flub where I crash into another car and for some reason my car flies literally 200 feet into the air.
I've had a lot of trouble with the stealth aspect myself. There is always lots of things in the environment to use, but every time I end up just going blazing guns. Aside from the missions that auto-fail you when you do this (which really pisses me off).
I'm enjoying the online play a ton, but I don't understand the scoring system at all. I can't find any logic behind it. I'll play online decrypt, our team will win, my kill/death ratio will be even or something like 6-5 and I will get negative points. Then I'll play another match, we will lose, I'll have even k/d and get 250 points. I mean wtf does it even mean?