Alpha Protocol is a role-playing game in both senses of the word. Levels, experience and stats are a major gameplay component, but it also allows you the chance to play your character the way you want. One of these elements works incredibly well, while the other pulls the entire experience down.
The overarching narrative involves the downing of a commercial airliner by a yet-to-be unveiled missile technology. As agent Michael Thorton, your mission is to uncover the masterminds behind the plot and hopefully save the world. It's typical spy-espionage stuff to the point of being cliché. Alpha Protocol adds some interest by offering playing control over how the plot will play out over time.
Story elements are spooled around Reputation, a set of dialogue choices similar to Mass Effect's conversation system. The difference between the two is, instead of choosing from bits of dialogue, you're instead left with three "attitudes" - Suave, Aggressive, or Professional. A fourth, usually violent, option is sometimes added as well. The system is a bit limited, but fun. Unlike Mass Effect, you're forced to make choices within a set time limit. It's a more "natural" way of handling conversations and encourages constant engagement.
It's cool, but the system is still in its infancy. While seeing how Reputation impacts the story is fascinating, it falls short on actually building a connection between choices and the player. Michael never grows as a character and always seems to come off as a smarmy jerk, regardless of reputation. Choosing "Suave" choices further degrades his character. He's isn't Bond, he is "Creepy Internet Guy."
Alpha Protocol places emphasis on choice, yet gameplay can feel really limiting. Some common templates, like a completely stealth-based character, don't work as well as they should, nor do they mesh into all gameplay situations. Much of the blame falls on stat-based mechanics. Alpha Protocol looks like an action-game, but plays like a dice-rolling RPG. Placing a reticule on a target and pulling the trigger is more for show. You're really just rolling the dice and dealing with THAC0 (not really, but you get the point).
Another reason for limitations are levels. Areas are well-designed, but boss fights force you into certain situations. Most happen in enclosed pits filled with an endless spawn of enemies, causing them to degenerate into shoot-outs. If your character is short on gun skills, you're in for long - maybe even unbeatable - fights.
Other than the story elements, I also really liked Alpha Protocol's handling of character classes. At the start you can choose from three pre-determined classes (combat, tech or stealth), or create your own "Freelancer." Another possibility is to go with a Rookie, who unlike the other classes, starts with zero skill points. The early game is hard enough as is, but playing as a Rookie makes it even harder. The pay-off comes in your second play-through, where you gain access to the Veteran class.