In my opinion:
Cap and Carter - Enough chemistry, but kind of generic and not extremely gripping. Did really like the ending.
Bruce and Rachel (Batman Begins) - Unique, chemistry that works for the angle. Also very well supported by the plot.
Bruce and Rachel (The Dark Knight) - Unique, but poor chemistry that feels stiff - but maybe the stiffness is appropriate given the story. Have trouble knocking it, even if I didn't like how Rachel's character was completely different from the last movie, in a negative way that made her utterly unlovable.
Bruce and Selina - By far the most chemistry. Also the most meaningful and fun. Wish they explored the psyche of it more (but this is true of 90% of the rest of the film). Otherwise, it was wonderfully written and acted.