I think it would make sense for Ultimate mobs to give more reputation/hate than in Elite or Normal/Vet since they’re always your level or higher, take substantially longer to kill and are deadlier than ever.
Ultimately, the best way to get nemesis status with a faction is to farm them in Normal or Elite once you overlevel them enough, but you’re pretty much fucked once you’re too high level because all that’s left for you to do is to farm Ultimate and that’s going to take forever.