One of my favourite games for the Genesis. It was my introduction to Shadowrun and to this day, I can't begin to describe how it moulded my conception of cyberpunk and my own writing as a result. It's one of three games that, in history, has legitimately changed my view of video games (Shadowrun for Genesis, Fallout 3, and XCom Enemy Unknown/Within)

Now, for your questions:

• You're not imagining the difficulty. I too recently tried playing it on an emulator and found it more difficult than I remember. I think it's because the slight lag on emulators between firing your pistol and it actually firing it is enough on the emulator that you simply can't win a fight. This (I'm guessing) is because of modern displays rather than old CRTs that it was designed for, kind of like jumping with Mario feels just a little bit different.
• It's pretty grindy in some respect. But that's kind of the reason that it felt so different to me back then. You're a Shadowrunner. You're doing jobs. Yes there's a quest, but it's one of the first games I remember where you could just ignore it for a while and punch a clock to go hack some corporation if you wanted to.
• Killing innocents is entirely up to you, Chummer.
• Samurai class is the all around'er. But I think Decker is the "canonical" way to play because decking is a fundamental part of the gameplay aesthetic.