Interesting bit they mentioned was torture and killing "...to protect the neighborhood". It would be interesting of certain decisions might have more immediately effective solutions (IE killing a gang leader) with further implications down the road (the gang was taken over by a even worse thug who has ties to an organized crime syndicate, which has allowed them to move in).

And that aside, I wonder how they will explain away death in this mmo? :P It's always a fascinating question... I feel CoX had an awesome explanation for death and revival mechanics, even twisting it into the plot now and then.

Finally, in regards to villainous things, in comparison between CoX (Mischevious, greedy, uncaring but not "want to see the world burn") and DCUO (You've unleashed trigon! Everyone will die. You've destroyed the water supply! You crazy SoB. Light some living cops on fire!) I would have to say that while DCUO gave you some options to feel truly villanous, they also sometimes took things too far, especially in cases where you have little to no options.
Alternatively, CoH you often did things that were kind good, but for greedy purposes. Rarely did you unleash some kind of evil upon the world (Without taking it down yourself) or attempt to kill a hero.

At any rate, I'm curious to see how they handle these things.

I'm more interested in how alignment will effect teaming.

Will the team leaders choices effect the alignment of my character? If they will, do I get a choice?

After the alignment system was put in place on CoH there was little that annoyed me more than answering a "lvl 50 team LFM" and halfway through a mission realizing that the team was doing a rouge alignment mission or any alignment mission that was against what my character's character :P

Will all missions have an effect on alignment? If so will there be a way to tell what the leader of the team is doing?

The answer to this may have a great impact on teaming in a city where all the alignments are mixed together in the same city.