Although I like it a lot more than many here do, the first recent thing that came to mind for me was
Sky Captain and the World of Tomorrow... the lack of chemistry between Jude and Gwyneth was the big problem.
Thats a good one. I thought that movie had it all, great effects, great story...concept. But you are so right; there is no chemistry between those two. A friend of mine has offered his take as to why that is, but because of its subject matter and sensitivity I wont go into it here; but it would explain a great deal. Maybe the same reason why I get no 'chemistry' in the whacko Harrison Ford movie Seven days and seven nights (though, in this case the reason is reversed on the leads)