A lot of those things he hates are... Pretty minor. I'll use black text so only people who don't mind spoilers can read it with their incredible color changing vision.
Spoilers:
"A Picture is Worth a Thousand Words" There's little you learn about the "System", but I don't remember it ever being explained in SS2 how you research things either. Presumably it has to do with your cybernetic upgrades, so your guy crams some mutant meat in to his head and eats some chemicals once in a while and the computer poops out information for you? Research camera didn't seem any worse to me than that.
"The ‘Special Edition’ screw-job" Making of DVDs are pretty worthless for almost all games in my experience. The soundtrack was disappointing, and though the big daddy figure is broken, it does seem pretty hefty and cool. Overall, for $10 more it doesn't seem bad, especially considering how expensive some other special editions get.
"The Ending Part 1" A little worse maybe, such as why would Tenenbaum save you after you'd been killing the little sisters? Presumably because you were the best choice to stop Fontaine. Other than that, it didn't seem any worse to me. Though Fontaine is more of a mustache twirler villain and not nearly as good as Andrew Ryan.
"The Ending Part 2" I agree on this one pretty much entirely. The end boss battle was a bit lame. Not game ruining but sorta annoying considering how cool everything else is.
"The Ending Part 3" He HATES the fact it doesn't roll in to credits? WTF?
"Interface Annoyances #1" Didn't really bother me. If he was playing on PC, he could check all his ammo levels pretty quickly by holding shift and mousing over ammo. Research camera bonuses I don't really mind as they seemed kind of fire and forget for me. Once you try to take a picture of something and it says all research complete then you're done. Power to the people upgrades are pretty easy to remember as most of them change the look of a weapon fairly significantly, and it should be easy to tell which weapons you've modded or not. If he wanted specific numbers then I definately wouldn't care. Do I need to know if the damage increase mod for the tommygun increases bullet damage 15% or 30%? Not really in an FPS. If I use the tommygun and want more damage I'd get it anyway.
"Interface Annoyances #2" I agree that being able to invent more than you can carry was annoying, I'll go with that. I didn't mind buying off security though, this was supposed to be an ultra-capitalist insane utopia, I can live with being able to disable security for money.
"Who’s Your Daddy?" That was kind of disappointing. Fishbowl camera, stompy feet sounds and 25% damage reduction. I did like the role reversal of the player being a big daddy and having to protect a little sister though, but I gotta agree it was a shame you didn't get a rivet gun or anything.
9 and 10 are really annoying. The copy protection almost ruins the game for me. Had it been less awesome and I wasn't looking for a day 1 purchase, I probably would've held off. Now that I already have it I don't really regret it, but I sure as hell won't trust any new games from 2K until I read about them now.
Sigh, and I thought I finally had some material for some article... 
