So, I haven't played the original Shadowrun, but the optional missions bug me.
The optional missions give karma, however, if you're playing an 'evil' guy, you won't accept those missions, right? Because you don't give a shit about a hobo or the friend of a dead woman.
If you're being a dick, can you still get those karma without being nice?
Think of it less as being nice and more of being reward driven. Sure a hobo may not be able to pay you, but they are often incredibly helpful information-wise. You aren't doing selfless acts of kindness, just very selfish acts that happen to be beneficial to others.
Also, I am 6 hours in and am really liking the story. The writing is well done and I really like the setting. I even find myself envisioning dialogue in my head like when you read a book, something that never, ever, happens from video games for me. It may also be worth mentioning I have never played a shadowrun game before.
Cons however seem to be the animations, as others have mentioned, the linearity of the story, and the fact that you are likely going to have to wait a while for the user generated content. I would estimate the campaign included with the game is maybe 12 hours? Probably less but I am being hopeful, so once you finish with that you are just going to have to put it aside until the mods start coming about.
EDIT: Oh yeah, and that whole checkpoint thing is great for the reasons Grumbs mentioned and isn't usually too bad as it is basically after each "quest" or whatever so it generally isn't too unreasonable to play checkpoint to checkpoint. However, it blows if you ever want to leave your game without leaving it open. I wanted to play for a little while before going to work and ended up having to quit mid mission which forced me to restart the mission when I got home from work, needless to say that was a total bitch. I have also missed the little thing saying it autosaved and have played way longer than I planned waiting for a checkpoint so I could go to bed.
Short Version: It has its flaws but is an enjoyable game for a cheap price with potential for endless user created campaigns giving you great bang for your buck. If you are extra cautious wait to see how much good user created content comes about before buying it.
Man I should review games for a living.