I was looking at the same choice last summer, and opted to go Model X.
My Model X came from FL, and I drove it home to the Twin Cities. It immediately went to Tesla for a check, because it wasn't charging at appropriate speeds, and they ended up swapping the pack. It was done under warranty, so not a big deal. I had a loaner Y for the three weeks it took my local service center to get the replacement pack in.
I would almost always choose the Model X. Sure, the Y has updated tech compared to my MCU1/AP1 Model X. Sure, it is under warranty for longer.
That being said, I find the ride comfort and quality to be VASTLY superior on the X. The seating is more comfortable as well. For the way I like/want to drive, AP1 is perfect. My kids (4 and 6 yrs old) are in boosters, and have more leg room in the X as well. The Falcon Doors are a dream for them getting in and out.
Where the Y has the biggest advantages, IMO, are range and charging speed. Generally, the range isn't a major concern for me. The X handles all of my normal usage habits w/o issue. Supercharging at a slower rate is not the end of the world, because I really just don't need to Supercharge that often.
At this point, based on what I paid for my '16 Model X P90D and what the price was at the time for a brand new Model Y, I'm happy with my choice. Based on the price increases the entire Tesla lineup has seen, I'm very very happy with my choice.