Seriously considering changing systems.

[blastingcap]

Sounds like you found the right answer.

After laboring for weeks about what the right direction for me is, I've decided on a refurb D7100 body.

The size doesn't really bother me; smaller form-factor of A6000 or other would be nice, but not necessary.

I want to take a pass at upping my photography skills, and more buttons and dials on the 7100 (over my 5000) should give me a fair shot.

And, the final truth is ultimately I just felt safer going Nikon, whether the 5300 or 7100. Safer = I know I'll be capable of getting solid results with enough technique and work.
And the A6000 shots I looked at ( and I looked at a lot ) just never wowed me. Admittedly, all of the shots I saw were posted by enthusiasts on DPR, but they just soured me on the system.

Yeah, handling is very important, something that gets lost online. If a camera doesn't feel comfortable/balanced/logical to you, you won't enjoy it as much. Since you already shoot Nikon, I am sure you will be right at home with the D7100 which has a bigger optical viewfinder, faster AF, more AF points, etc. And more custom controls and less menu-diving. My D5100 is good enough for my purposes (low light + non-fast-action) that I don't feel like upgrading yet, but when I do, I might get a D7100 down the line, too.