They are both acceptable. I think the first would be more natural with "with three generations".
Are the sentences below acceptable, or natural? Thank you.
1. The major problems of three generations living in the same house are their different living habits and schedules.
2 Different lifestyles and schedules of family members are the major problems with three generations living in the same house.
I would delete "of family members" in the second. That's clearly who you are talking about.
I'm not a teacher, but I write for a living. Please don't ask me about 2nd conditionals, but I'm a safe bet for what reads well in (American) English.