Aside from "The Best of Both Worlds", "Chain of Command" is easily the best two-parter in TNG's run. Though not as fast-paced as its predecessor, it projects the same tense, militaristic feel and doesn't offer a lot of breathing room. The idea of a by-the-book captain replacing Picard at the helm of the Enterprise is an inspired one, and it works particularly well in this context (tension rising with the Cardassians). It's enjoyable to see Jellico putting the Enterprise crew in their place - expressing little patience with Riker's insubordination, telling Troi to stop wearing her silly little outfits, and even telling Picard "it's my ship now."
The secret mission is probably the weakest part, simply because the cave set is not particularly interesting. But the shock at discovering that the mission was a set-up, along with Picard's capture, make for quite a cliff-hanger.