I'll get this straight right from the off: Alpha Protocol lacks polish. That being said, a huge replayability factor, a compelling cast of characters, and a unique conversation system delivering well-written dialogue all contribute to making those faults easy to overlook.
A huge positive in Alpha Protocol's favour is the significance of choice. The stances you take with any given character can have effects ranging from the presence or absence of available intel for a selection of missions to your reputation preceding you when dealing with new acquaintances in the future. And nearly everything you do will be scrutinised by someone at some point; by your handler during a mission, for example, or during the flash-forwards after significant events.
Criticism of the game for lacking polish is not an argument without merit. However, be wary of what these criticisms are aimed at. Try not to be fooled by the outward appearance of the game; it is *not* a cover shooter in the vein of Splinter Cell: Conviction or Gears of War. Obviously, taking cover during a firefight is a good idea. But the crucial difference is that in Alpha Protocol player skill is not a valid substitute for Mike Thorton's ability to aim within the game's mechanics. It is an RPG, and as such if you haven't put any ability points into the Pistol skill (for example), don't expect Mike to hit anything very often when using one.
That isn't to say that the game is without legitimate flaws. Animations for actions such as stealth takedowns and kills are limited and repetitive. Enemy AI is rather dumb at times as well, and some of the higher level abilities are ridiculously overpowered (a combination of Shadow Operative and Chain Shot will see you through each boss encounter without exception). Although I have to admit with the latter that it can be good fun to feel like such a badass superspy, as no matter which collection of skills you choose to specialise in you are practically guaranteed a strong build rather than accidentally handicapping yourself out of inexperience.
And let me just add on the subject of boss fights that the encounter in the disco ballroom to the tune of Autograph's "Turn Up The Radio" was inspired.
It was recently announced that Alpha Protocol would be not be receiving the sequel treatment. For me, and the many others who thoroughly enjoyed the game, this is sad news. I do hope, however, that the base mechanics and conversation system are used at the least as the backbone for a new franchise with the polish they deserve. There are simply too many good ideas to be found here for me to want anything less.