Thank you all guys for answers!
I have had both cameras in my hands and I don't really care about the size.
When it comes to the system, my friends have Nikons, so we could share lenses. On the other hand I could use all my old m42 lenses with Sony via adapter.
I really don't like Sony's EVF but I know it might be useful.
I also don't mind not being able to change aperture in Nikon's live view.
In fact important difference for me is better image in d5300 (really love it) and peaking in alpha6000.
In general I would rather buy Nikon but I still have Andrew's unfavorable review http://www.eoshd.com/content/12111/nikon-d5300-review on mind.