Omer-
LEED for New Construction would be used for both the hotel and the residential units assuming it is more than seven stories of residential. They use the same rating system so I don't think you have a good reason to split them into two LEED projects.
USGBC typically follows the 40 / 60 rule for determining project certification. If 60% of the project SF falls into one category then that rating system should be used. It is ultimately up to the project team to make the case for the chosen rating system.
My suggestions would be to calculate out the different “types” of SF in the building. If any “type” is equal or greater than 60%, I would use the rating system. If there is not a clear winner in what category of LEED to use, I would look into submitting a CIR.