Hotel Dusk.
Damn, beaten to the punch. I just finished replaying Hotel Dusk and Last Window back to back (Hotel Dusk's localization was handled by NoA, Last Window's by NoE) and it was striking how much more natural Hotel Dusk's script felt. Last Window's wasn't bad by any means, but Hotel Dusk's script was just so much more lively.
A good example is when Martin is talking to Kyle and says something along the lines of, "Yes, Mr. Hyde, I have deduced your true identity at last!" to which Kyle thinks "Maybe I should deduce my fist to your face. Bet that'd shut you up." I obviously can't say for sure without playing it in Japanese, but that feels like a moment where they opted for something more in Kyle's character rather than a direct translation of the Japanese script.