Why did apple filling in the pie turn to mush? I'm not talking about the crusts. Those came out fine. 

But the fruit of my apple pie came out dark brown without any crunch at all. They turned to mush, like a thick pudding or sauce.

I used 2 pounds of Granny Smith apples sliced thinly, 3 teaspoons of lemon juice, 1 teaspoon allspice, 0.25 teaspoon salt, 0.25 ground nutmeg, 0.25 teaspoon kosher salt, 2 tablespoons all purpose flour, 2 teaspoons ground Saigon cinnamon, and 0.75 cups of sugar. 

I didn't cook the apples on a pan, just mixed the apples with the sugar and the flour and allspice and stuff and let it cook in the pie in the oven for 90 minutes(the first 30 minutes at 375 degrees and the 60 at 350 degrees.
Hold back a bit on the lemon, or toss 1/2 teaspoon of baking soda in the filling. I don't see any other cause for the apples to have completely macerated in your recipe other than the acid content to cooking time. 90 minutes is a rather long time, but I'd expect them to hold up quite a bit better than 'mush'.

You could also try blind baking your bottom crust for 15 or so minutes so the final cooking time is shortened, which presents less opportunity for the apples to soften. Ideally, you want to be in the 45 minute to one hour range. 

If it were me, I'd probably try both. Keep trying and experimenting, bringing a fresh pie to the table is one of the most satisfying ways to delight your friends and family :)