I have a similar problem, and have been waiting, hoping I might find an answer here.
My tree looks and sounds the same, only difference I do have a small amount of fruit forming.
I believe it's a form of Iron Chlorosis (sp). I read somewhere caused by lack of full fruiting. Didn't make sense at the time, so I still wait for another answer.

Not too long ago, Olpea (I think) gave an answer with a link about this yellowing problem of Honey Crisp. I can't find that thread at the moment.

It seems yellowing is one of the characteristics of Honey Crisp. It does not hurt the tree. I also read that HC trees that have more yellowing are not productive.

Mine is about 7-8 yrs old and just fruited this year (talking about non-productive!!!). There are only 5 of them on the tree now. They are so big, a couple seem like they are about to burst out of the plastic bags I put them in.

I've read many times here about Honey Crisp' leaves look ratty, yellow, brown, etc. Mine fits that bill, too. It's been like that all along so I let it be.

My Honeycrisp looks similar...while apple seedlings right next to it look perfect...its just a crappy looking tree.

Rehabbing,

That looks like it could be Honeycrisp yellows. Below is the thread to which Mamuang referred.

The mottling looks somewhat similar.

Here is a link that might be useful: Strange foliage discoloration on Honeycrisp

Looks like a Honeycrisp. mottled leaves, cedar rust, and gangly.

We plan to move to an acreage in the next two years and I have a plan for Honeycrisp. My wife loves them, due to the sweet and crispness, but I don't like them so much due to the lack of actual flavor. Anyway my plan is to take reliable trees like Liberty, Enterprise, etc and graft 25% of each tree to Honeycrisp. So let the stronger leaf system of the other variety prop up the HC portion, but leave plenty of the other so it does well too. This is just a thought. I've not heard of anyone trying and proving the theory.

Our current HC tree I grafted Enterprise onto last spring. Those leaves are still lush and healthy and the HC are all beat up by bugs and cedar rust, so next year will add some more grafts. If we are here long enough I'll graft something else to the main leader at like 10'. Keep the bottom HC and something with resistant and strong leaves up high. Although this year I'm bringing the leader down a couple feet and keeping it HC.

Thank you all so much! Wow, these trees are really a pain in the rear. I'm sorry everyone else is going through it too but I'm glad to know I'm not alone. I guess I'll just leave her be and see how she does next spring :/

I visited a friend's house (in Zone 5a). He has a 3 years old Honey Crisp apple tree in the backyard that was loaded with apples, almost an apple at every node and at every part of the tree.The owner was surprised too by the heavy crop. No thining waxs done and the size was the same as one see in the stores. It was sweet and very crispy.
I started thinking of planting one too coming spring.

After reading many posts on HC apple, some have no problem, others, I included, have had a problem with slow production. Ratty looking and yellowing leaves seem to be a common issue. I wish you luck.

Please check with your friend next year. I would be interested to know if his HC would become biennial after bearing so many this year. It is quite possible.