As for the chemistry between Luke and Lorelai consider what we've been used to for all these years between them and how they still act with each other when they aren't in bed... she "annoys" him, he makes a smart comment, she makes an ever smarter comment, he goes away to get her more coffee and she continues making smart comments about Luke to whoever she is sitting with (usually Rory, but hell, even Kirk will do). And we've always loved this. The two actors work wonderfully well together in this regard. It's fun and flirty. They have undeniable chemistry, or at least, the ability to play off one another, in these scenes. I wonder, Duds, what exactly do you expect of them in their alone time? More of the this? He can't pretend to be grumpy when they're postcoitally sitting in bed -- after all, them being in bed together is what he's always wanted.
May I also mention the wonderful scene from last year in which the two finally go on a date. They go to some restaraunt we've never seen before. As Lorelai describes it, this place is "Luke's Luke's." That is, it is to him what his diner is to her. Something this scene so wonderfully does is that it simultaneously establishes Luke's independence from Lorelai (she didn't seem to realize that he ever left Luke's) and his admitting (through the horoscope in his wallet) that he is completely fascinated by her. Since then, in their relationship, she is no longer just some sexy, funny lady who likes his coffee. She's still that, but now, as his fiancee, she's so much more. The lack of chemistry you describe is what I would describe as recognition that there are no more obstacles preventing them from being together. There shouldn't be a tension there, so there isn't.
Now that the writers have created a new tension, that of the daughter, things may be awkward. And I will admit that I don't care for how the characters have thusfar reacted to her. Luke, as blown away as he deserved to be by the discovery, would have told Lorelai. Had he, Lorelai would have, in character, wouldn't have had any problems with it. So that's my big complaint with this new storyline.
I do, in principle, like the creation of the new character. Luke has always, in a sense, wanted to be Rory's father. He thought she was too good for his own nephew, for instance. Christopher, meanwhile, has never been good at being Rory's father. He always seems like such a great guy until his lack of stability or reliability takes over. Now, Christopher has another daugther, who, like Lorelai had to with Rory, he must raise alone. This is such a difficult task, and he's not doing a very good job. Gigi is a spoiled brat. Now that Chris is ass-backwards in money, Gigi will likely continue to be a spoiled brat. Yet, at the same time, Christopher wants to do something for Rory, to finally be there for her, so he pays for Yale. Thus Chris is finally there for Rory, but he isn't really there for Gigi. Luke will always be there for Rory, and not just with a hot pot of coffee. He loves Rory like his own daughter. But now, like Chris, Luke also has his own daugther, independent of Lorelai, and it really bothers him that he hasn't been able to be a part of raising her. But he thinks he should be there for her now, even though the mother (who seems to be doing a wonderful job raising a mini-Rory, and if that parallel isn't enough, if I'm not mistaken, the mother is also a small business owner, selling something or other from her home, but I could be wrong about that one) doesn't really care.
The parallelism is interesting, and it hasn't been handled perfectly, but I haven't given up on it yet.
Man is a giddy thing, and this is my conclusion.