IN regards to "Emissary" Being a great pilot, don't forget the major amounts of forshadowing that went in there, if I remember correctly, the Prophets tell Sisko that his is "Of Bajor", and what do we discover many seasons of the show later...that he is ever so slightly Bajoran!
"Encounter at Farpoint" is another good one: The flagship of the FED is sent to negotiate a treaty with the Bandi, only to run afoul of an near-omnipotent being! Watching the crew negotiate the mysteries let's us see what the NG era will be like: multi-racial (and species) crews, more thoughtfulness, more powerful tech (that often makes things easier for the crew...except that holodeck!) but somehow more focus on the human condition than TOS. IMHO (which i capitalized, showing my humbleness!)
So, what's your new campaign like?
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"Yes, it's the Apocalypse alright. I always thought I'd have a hand in it"
Professor Farnsworth