Eh, they aren't as similar as you say. Deus Ex is a totally unique game even to this day, and while Alpha Protocol shares story elements (conspiracies, exploitation of people by large corporations, etc.), and gameplay elements (can choose stealth or combat approach), Alpha Protocol is also much more mission-based, linear, and gives you far fewer options for solving situations. It definitely excels when it comes to character interactions and the potential for shifting allegiances is there, but as far as gameplay goes, Deus Ex is far more of a role-playing game in my eyes. Whereas Alpha Protocol puts you in very particular situations and gives you clear goals, Deus Ex is all about dropping the player in a large, open environment and then letting the player figure out how to accomplish objectives. I don't think you can really directly compare the two, but Alpha Protocol definitely scratches the same itch for action role-playing.
I actually came into Alpha Protocol right after my first play-through of Deus Ex: Invisible War. I'd put that game off for a long while due to all the negative comments, but in many ways it's quite a bit like Alpha Protocol - it's got both technical issues and slightly dated visuals, as well as the ability to ally yourself with different parties, often who have conflicting objectives. I think, looking back at the reviews, Invisible War probably got the sorts of scores it deserved, but only because it was a sequel to Deus Ex - had it been put out as an original title, not attached to such a famous name, I think people would have accused it of being a buggy, unplayable mess. It also makes me wonder what sort of scores Alpha Protocol would have got if it was a sequel to another successful game.