Chemistry is exactly what it sounds like. It is a chemical, hormonla physical reaction that occurs when one is attracted to someone. If a guy is not feeling ANY chemistry after two dates (and I mean ANY), then it probably is not going to happen, because guys react hormonally more quickly than girls do, as a rule. Hashem designed us that way. That said, when a guy tells a shadchan there is no chemistry, it is often his polite way of saying he doesn’t feel she is attractive to him.
Girls may use the chemistry excuse, too, but a girl gets attracted to a guy for many different reasons, and looks are only one part of the equasion. I think a girl will go out for additional dates when she sees a potential for attraction. I think guys would say buh-bye after no more than two such dates.