I've beat it way too many times and my favourite way to beat it was my first way. I started out as a recruit and put all my points into stealth first (keeps missions interesting) and pistols (Chain shot is a one shot on most bosses and making criticals while still in cover ). After finishing those off I just randomly threw some in martial arts or w/e.

 

In Hind sight I think I should've put one point for interference because the hacking becomes really hard. *SPOILER* when going back to AP it makes it so much easier is you have smgs and some points since stealth doesn't always work there.

Sorry I don't have exact numbers but just throw them all in three and then you just run around levels invisible and one shot people from cover.

 

I only had to buy the tactical stealth armor(must save Sis(who is strangely attractive ) since it's from G22) and I stopped buying intel once I hit rome because they do help but not that much.

My favourite so far is Stealth/Pistols/Sabotage, with a few points to SMGs and the first 3 levels of Toughness - adding 50% to your base health is well worth spending 12AP on, but I rarely get shot/hit enough to need even that much. I guess I just like to have that extra bit of a safety net...

 

Basically, I try to stay mostly invisible, but when things go wrong at point-blank, my SMGs can fix the problem.

My last replay that I just finished, playing as a Recruit, I decided to max out pistol, assault rifle, and sabotage. It seems to be an effective build for both stealth and run-and-gun. My pistol (with silencer) allowed for a lot of quiet kills, but my assault rifle ability also allowed me to exchange long range fire the times I was caught sneaking around. And sabotage let me hack into any computer, pick any lock, and disable any security system with ease.

 

I might try a stealth build next, but I'm not big on sneaking around. I'll do it for the most part, but if there's a room full of enemies and it looks like it'll be very difficult to sneak past, I just open fire.

Pistols + Tech Aptitude + Martial Arts

 

Assault Rifles as secondary weapon.

 

It's quite satisfying drop-kicking people in the face and chain-shotting everything to oblivion.

I always love playing through Alpha Protocol with different builds, just to see how well certain abilities mesh.

 

My initial build was (and all the ones I list initially will be the ones specialized in) Pistols, Stealth, and Assault Rifle.

Most efficient build was Sabotage, Pistols, and Technical Aptitude.

Current Favorite is Martial Arts, Sabotage, Stealth.

 

I feel the second build is the most efficient because, and let's be honest here, you'll never need anything other than pistols after getting Chain Shot, Technical Aptitude just gives you a whole mess of goodies, and Sabotage allows you an easier time in hacing and lockpicking while also giving some decent abilities. The third build is my current favorite due to an idea I had while browsing the internet one day: that of a close quarters, near invisible assassin with a heart of gold. That I can actually play Thorton to fit this character I conjured brings me no small amount of joy.

 

I really couldn't tell you why I like the first build, other than that it was just how I played it the first time through and it stuck with me because of it.