Personally, I prefer Scott and Jean.
Sadly their relationship was greatly damaged and dare I say, sabotaged due to many factors such as Jean's resurrection after Dark Phoenix Saga, Scott abandoning Madelyne Pryor, Scott getting darkened thanks to Apocalypse, the third wheel that was Wolverine, Grant Morrison's run which basically just intentionally strained the couple's relationship by making both partners cheat on each other. To me, they were both written way out of character during their "marital troubles" phase.
Emma, after Jean died was kinda reduced to a Cyclops cheerleader. Her whole theme was All for Cyclops. That's what it seemed to me because I stopped reading X-Men after Jean died her last death.
But I want to know what everyone here thinks and maybe get some POV's about which coupling is better and why. There's probably been this type of poll before but... whatever.