I watched all these episodes as they aired so I had the comparison thing going on back then. Sometimes one show would be the clear victor. Other times not so much. Sadly, other times, both episodes were less than perfect. I think they could have done better crossovers though; I'd have enjoyed a more in depth crossover event. I like that kind of stuff.
-Darker tone: Some have said Chain Of Command: Part 2 is TNG's darkest hour, a fair assessment considering half the episode is of Picard being tortured. If the producers were hoping to prepare the audience for DS9's darker tone here, they certainly succeeded.
The Chain of Command 2 parter was initially meant as a crossover with DS9. The Ferengi that Crusher seduces with her possible 'gratefullness' was written as Quark, but then it became clear that these episodes would air before
DS9 started and the role was rewritten as another character.