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In Alpha Protocol, there is not really an open world. It's all mission-based, so anything done is progress. I want to go through the game like a bad-ass, superpowered, but I can't find any spot where there's something like indefinitely respawning enemies to "farm". Is there a way, other than Veteran?

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Yes, there are ways. The two main sources of grinding are orientations and a computer on Lazo's yacht.

You can repeat the gadgets and stealth orientation for XP. I recommend gadgets over stealth for XP, because I think that, on an enemies defeated over time basis, it's more efficient. Repeat of the dialogue allows grinding certain dialogue-based perks (see below).
How much time will it take? Each enemy subdued is worth 10 XP. Just taking a sample between two saves: at 05:47: 40210 XP. At 02:20: 37490. 40210-37490 = 2720 XP. Time elapsed: 3 hours and 27 minutes = 207 minutes. 13.14 XP per minute.
Be warned, difficulty scales with AP earned, so you'll get tougher mini-games too.

Which perks can be grinded? Shock and Awe, Building a Deadlier Mousetrap, Perfect Pitch, Lurker, Surprise attack, Black belt, Limited Bloodshed, Merciful, Pistol Proficiency, Pistol Mastery, Tough as Nails, Insurance Liability, Hard to Read, One-Track Mind, and Testing the Waters. There's also one or two hacking ones, but I think I skipped them because they're just XP. Building a Deadlier Mousetrap and Perfect Pitch only reward XP too, but I got them incidentally.

In Mina's bonus challenge, you can farm Pistol Proficiency and Pistol Mastery by shooting the body. Here, you can also farm tranq. ammo. It takes 15 seconds for the ammo to respawn. 12 tranq. rounds go for $50 each, but they cost much more to buy, and they're commonly out of stock from vendors.

While you can farm ammo slowly, it is most efficient to farm cash during the mission "Assault on Lazo's yacht". This is a glitch involving an Alpha Protocol version of the hack reward accumulation glitch. It requires any tier of the Improved Data Theft skill in the Sabotage line. Only two devices are known to allow this to work, and the earliest is on Lazo's yacht in Russia.
Hack the laptop below deck, die, then reload last checkpoint until you are satisfied with how much that you've stacked up. It will not work if you load last checkpoint before death, only when you reload last checkpoint from death. Each subsequent hack will earn X*(1+Y), where X is the amount earned from the last time that you did this hack, and Y is the cash bonus percentage from Improved Data Theft. The game glitches at some point beyond $1.86 billion dollars, so I suggest that you don't stack past that. To buy everything requires one or two ten millions, IIRC.

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