Alpha Protocol is a great game. It does have some flaws (without which it'd be an awesome game). And the PC version suffers a bit from having the settings tuned down to match the console versions. With a bit of tweaking the .ini files, the game looks much better.
Many of the scathing reviews seem to be looking at it from an FPS (or Mass Effect 2, which is more FPS than RPG) perspective, and sure, from that perspective the shooting and AI is underwhelming. But that's the point. It's not an FPS, it's an RPG, and your shooting abilities are supposed to suck until you put enough points into them. When you judge it by the appropriate standards, it's excellent.
(Interestingly, most of the PC reviews that I've seen have been fairly positive; it's the console reviews that seem to be dragging the scores down.)
And the dialogue system is great (although he's right that it does suffer from Mass-Effect-itis, where what you think you're going to say doesn't always mesh with what you actually say, although the JB triad does always give you a hint of the tone you'll use).
The Brayko boss fight does suck at first, especially for stealth or melee focused characters. But you should never focus exclusively on melee -- you should always have some points in at least one weapon. Then it's just a matter of learning his attack patterns and working out when to attack and when to dodge -- just like every other boss fight ever. (And, if you have the right contacts, you can dramatically shorten this fight.)
