Things I prefer about Disneyland:
1. More rides in general, especially in terms of smaller FL rides, plus more E-tickets (Indiana Jones, Star Tours). And just the general density of the rides that they are kinda on top of each other.
2. Smaller footprint, so it is easier/quicker to get around
3. More larger scale entertainment offerings, in particular having Fantasmic! there
4. Better/more kinetics, such as in FL, the subs/monorail/Autopia and around the RoA (though MK does have the Peoplemover and elevated Astro Orbitor which are plusses for it)
5. Better/more varied in park food (though MK, once Skipper's Cantina opens, will largely close the gap, I think)
Things I prefer about MK:
1. Much wider pathways and less crowding. As terrible as it can be getting around MK certain times, it can be worse at DL
2. Better isolation of the different lands with isolated more immersive theming
3. More/better shows
4. the presence of the interactive games (I understand they are not everyone's cup of team, but I think the Pirate one in particular is quite nice)
5. Generally better queues that enhance the ride experience
I think the quality of cloned rides is relatively a wash (both have their share of the "better" versions).
As I said, I prefer DL to MK. However, I am curious as to what is in store for MK in upcoming years -- with ~$350M supposedly earmarked to the park and the possibility of a Frontierland expansion, MK could easily close the gap between the two. But in the meantime, DL will get Star Wars which will probably push it out ahead again.