While all ME games are far (far far far) better games than Sega's "esponage rpg" Alpha Protocol, AP was able to do something that ME could not: in AP all your choices really did matter and changed both the game and the endings. The permiatations of who might end up being the real bad guys (depending on who you choose to aid/grow close to), and so engendering different motives which implied different world events, was pretty mind boggling. I can't think of any other game that has come close.
That being said, it seemed like developer Obsidion put all it's effort on that and little on the gameplay. It's repetitive, sloppy and buggy. I remember trying to race through missions so I could get to the dialog & NPC segments.
Maybe someday someone will be able to successfully combine the two. But for now, I'd suggest playing ME3 and pretending what you did as Shepard mattered.