Yeah, kids change it all don't they!!?! ;) I certainly don't think you two are doomed, but eventually you'll need to get on the same page. I have many of these same struggles with my husband. I think the biggest issue is that they are men and don't get it. I know that this is a stereotype and I know that ALL men aren't this way and frequently moms on here get huffy when someone lumps men into categories but I'm going to take my chances!
Anyway, my husband doesn't pick up his own laundry and put it in the basket, he doesn't clean up his own dishes nor pick up anything that he might accidentally knock on the floor. It drives me up a freaking wall. So, when the kids do it, he doesn't notice it then either and therefore doesn't help them to correct it. I think that these behaviors in my husband are more typical for men than not, but that doesn't mean it doesn't annoy the hell out of me. Nor does it mean that I should accept it and move on like I don't get annoyed...BUT, there is a time and a place and you have to pick your battles with him.
I would suggest that at another time completely, mention to him that hey let's remember to have Daughter put her clothes in the basket when she puts her PJs on b/c I think we should work on that skill with her. Or something like that! If you do it a few hours or a day later he won't get so defensive, hopefully. Also, make sure you praise him thoroughly for the help he did give you and things he did do. This will make him happier and more inclined to hear about the things he needs to add in next time.
Recently my husband and I had a discussion about our bedtime routine too and he does it differently than me, which in and of itself is not a huge deal...the problem was that he was letting my 4 y/o completely and totally manipulate him. Anyway, I was irritated b/c it also made more work for me when he gave into her every demand and I didn't. He got really mad at me when I brought it up, etc., etc. but then one night he put his foot down and started being consistent...and wouldn't you know it, a week later he made the comment to me about how much better she'd been acting. LOL!
Oh my gosh, I totally feel like I'm rambling here and my message is getting lost! It's been a long day! Okay, my point here is that you are not doomed and that you just need to talk. Try to be calm and nice b/c he really does think he's helping, even if he's not. Work it out and come up with a plan so that you both feel good! You'll have good days and bad days I'm sure! Sorry for my babbling!!