I just finished Alpha Protocol and boy was I impressed by a lot of it. there are several things that it did much better than Mass Effect 2, mostly relating to story and characters.  
But what I found was the best part about Alpha Protocol was how much my impact was felt in the world. Right now I feel like I can overlook some of the jankiness and the poor shooting and say that I enjoyed it more than ME2. I really liked the fact that there was entire missions where you don't even shoot anyone, and it had a real plot, not just grab some party members and go fight some people. 
 
So does Sega own the IP for this game or does Obsidian, because if Sega doesn't own it I could possibly hold out for a sequel some years down the line, which would make me very happy.

On the contrary Obsidian has come out and said they are not done with the franchise.  (i don't have a link on hand)
Sega was just a publisher, they don't own the IP.

I think I got a little something extra the first time (well second time, but you'll see) I played it. The thing is I really like to screw around with config files. Tweak settings so that everything is pretty. Of course AP on PC already looks great, so I just decided to force some supersampling AA through Inspector and see what happens.

Cool thing is AP also runs really great even on older PCs. An Unreal game done good in the sense, so adding some extra bells and whistles only made the experience better. There was a drawback though, which at the time I didn't realize. Forcing AA made the conversational button prompt text disappear. So, the first 3/4 of the game was me pushing blank button prompts getting completely random outcomes.

I couldn't see what I was going to say in conversation, so I figured the prompts were morality buttons instead or something. Of course that isn't the case, so my story went in every which way, and it I couldn't decide if I liked it or not. I can't remember in the QL, if Jeff did any conversation stuff, as I mostly remembered instantly being enticed by the menus . So a little uninformed, it got me thinking that's how the conversational stuff works in the game. I reluctantly rolled with it.

Bored, I searched around for more tweak guides, and see if I can screw it up in anyway. Turns out I already managed. Turned off the AA, and wow, that game instantly turned cohesive and awesome. Even though I finally got what was going on a little too late, the game became even better and I exploded with joy.

So, dear reader, I decided to play it again. It was like I watched a movie, but I didn't like how it went. Now it was my chance to truly get behind the wheel and experience what this game has to offer.

Oh, and I played it all with a 360 controller, and it was fucking wonderful.

It also could have been like ten hours longer too.

Hah so yeah to the OP, I would appreciate another game! :)