The default gender field from XF1 was migrated to a custom field in XF2 if you upgrade from XF1. A clean install of XF2 doesn't include it at all.
Obviously the flexibility of moving it to a custom field means that anyone who already had the gender field from XF1 can now customise it as they see fit to cater for more identities, and more suitable wording.
Also now it's gone from the core software, if anyone wants some sort of gender/identity field then they can just create their own, without having to remove the old default one from templates etc. as would have been the case in XF1.
You make a valid point - should we still have it here? Maybe not, but it does at least demonstrate the availability of custom fields in general.