I've convinced myself into the Sony a6000 over the Nikon d5500, although for sub-$1000 camera bundles these are miles ahead of what was available not that long ago.
I think the sony will get more use being smaller and lighter. if it feels too small, i'll add a batter grip.
I like that its faster for action photography.
image quality and focus seem to be the same or a slight edge to sony.
sony is about $200 cheaper comparing similar bundles.
the disadvantage of the sony is its seems to use battery life twice as fast, but that can be overcome with a $50 spare.