One big difference I've noticed is regressions. While Dolphin has an insanely strong regression suite and plenty of people testing for regressions, Cemu seems to randomly go back and forth on support for games.
If you look at this unoffical "change report" you see a lot of comments mentioning that: https://www.reddit.com/r/cemu/comments/6d3nwc/180_megathread...
Part of it is probably how early in the game it is compared to Dolphin, but part of me wonders if being closed source means it's development won't ever reach Dolphin levels of quality