Of the two I'd say Eleni, because Emilia Iris is a mouthful.
I think both are going to run into pronounciation/spelling issues, though... Emilia is going to get Amelia all the time, Eleni I think people will trip over 'e-LAY-ni' and 'ELL-uh-ni'. Not insurmountable but annoying (as someone with an-often-misspelled/said name).