I can't hear him cracking too many jokes in the Hive level, if that's what you're referring to. He says a few lines ("Why do they always take the hot ones," "Looks like you're fucked") which some people might not approve of in that context, but I'm not very sensitive about it. If anything I think he sounds pretty sad and angry about the whole thing. I'm not very happy about the fate of those women either, even though it's just a silly game. Anyway, it's Duke Nukem. It's supposed to be a bit silly, in my mind.
I agree that the game has its flaws and I wish it was more like Duke3D and less like Call of Duty, to put it that way. I still enjoyed it, though.