Motion at Sea
I''m no designer/architect but in my experience *in general* (and all other things being equal) the flatter bottom boat will be more uncomfortable. The deeper ''V'' hull will cut thru the water better where the flat bottom boat will tend to ride on top and pound more in a chop.
But as the others have said there are a lot of other factors to consider (even beyond the boat itself). There are conditions where the flatter bottom boat would be more comfortable than the deeper hull. So take my VERY generalized statement with a grain of salt.