I’m just not fond of unisex names, so I would go with [name_u]Elias[/name_u] and call him [name_m]Eli[/name_m].
I also like that [name_m]Gideon[/name_m] and [name_u]Elias[/name_u] both have 3 syllables.
This makes me wonder if [name_m]Gideon[/name_m] has a NN.
[name_u]Ellis[/name_u] is a very pretty name, but you may find yourself calling him [name_f]Ellie[/name_f] in no time!