Well, sure, Kelly and Scotty as Numero Uno pair. Goes without saying!
I DEFINITELY agree that John Steed and ANY of his partners--Gale, Peel, or even Miss King were great Agents.
I absolutely agree with Tatia's idea of Mission: Impossible and the Wild Wild West's West and Gordon being great spies.
I don't think it was that Maxwell Smart was that great a spy, just that the Chaos agents were as inept as he was!!

)
I would also include "The Equalizer"'s Robert McCall, even though we saw him mostly after he retired from being a spy. But, we all knew he was a Master Spy and a Master Equalizer.
I'm not adverse to MacGyver except it was such a boring, one-dimensional role for Richard Dean Anderson. His character was an exceptional agent, but he was also the least interesting personality, with none of the complexities and flaws of Kelly and Scotty. The combination of being superb spies and superbly complicated and fascinating characters is what set I Spy ahead of other shows.
Never watched "Man From UNCLE". Never cared to--neither character rang my bell at all.
My two cents!
Mona