I love good chemistry. But I think what really sets good ships apart from the rest is the relationship the characters build. I love the friendship/partnership first where the characters eventually get together after forming an unshakeable bond, trials and tribulations, and a great deal of “almosts”.
For this reason, I think the best pairing is Booth and Bones in the show Bones. The characters start out with animosity between them, develop an understanding, then friendship, then something that everyone else is calling a relationship (but the characters aren’t physical with one another) then (after trials, tribulation, and sorrow) they finally end up together. The show even managed to continue on for another SIX seasons as their relationship continued to develop as they got married and had two children. Most couples lose the sizzle after they are together, but they continued being adorable because they still bickered and teased each other and they still operated as one another’s foils. He was the “heart” and she was the “brain”. They weren’t opposites—they united by their sense of justice, and they were both struggled with their family histories. But where one of them struggled, the other was strong. And they pushed each other to grow in those areas.
That’s what makes a ship eternal. Two people we initially like because of their banter and their chemistry but then we fall in love with because they really are suited for each other. Chemistry without that relationship of mutual benefit just ends up being like cotton candy—sweet but lacking substance.