Equipment assignments are done to minimize operating cost.
Direct flights are just marketing ploy. e.g. NW has a "direct" flight between JFK and HKG, with a "stopover" in NRT. Note that CX also has "direct" flight service too; however, they've been wanting to do non-stop service.
I once flew ORD-MNL "via" NRT on NW flight 3 about 15 years ago. The funniest thing: I missed the continuing flight because of a mechanical delay.
Note that by chosing "direct" flights, you only get the mileage A->C vs. mileage from A->B->C.
If I ever come across an option for a direct flight, I'd break it up into two segments.
- Pat