PM here and I haven't flown in a middle seat all year.
A few questions:
1. Do you do your own bookings and pick you seats when you book? I assume you're not booking basic economy.
2. Are you selecting complimentary C+ upgrades at booking?
3. How far in advanced are you booking?
For myself, I do the vast majoring of my bookings no more than 3-4 days in advance, and often times within 2 days of departure. I look at the seatmap for every segment and make sure there are non-middle options. On more than a few occasions, I've taken longer routings/connections to avoid a long segment in a middle seat. I also look at C+ availability when I'm booking and will only select the upgrade if I'm confident it will put me in a window or aisle C+. Otherwise, I wait til check-in when I can select window/aisle only C+ upgrades. TATL journeys I usually am able to book a little further in advance but not much, and again have had no problem, so it just seems like your ATL-AMS is especially full in Y.