Good food for thought!
I think that the 3500 calorie rule was determined in a lab in test tubes, and you're so right, we are WAY more complex than that!! There's no way that number can be correct for everyone.
As someone who has maintained a 100 pound weight loss, I have to say that it was confusing at times (like many people) when you are doing the "math" of calories in v. calories out correctly and not losing. There are other times when you aren't doing everything "right" and lose.
Genetics, metabolism, stress, sleep, emotions, depression, HORMONES, water retention, nutrition, macronutrient breakdown, exercise, etc. all play a huge part in how each person gains/loses weight. AND it's different for everyone. That's why there's no one-size-fits-all program IMO.
However, I KNOW that MY body responds to watching portions, eating healthy fruits and veggies, lean protein, lowfat dairy and complex carbs. Drinking water is huge for me and I drink at least 3-4 liters of water a day. Because of my crazy work/sleep schedule I don't eat a traditional breakfast. After waking up, I wait until I feel true hunger (usually 3 hours or so) and then I eat every 3 hours or so after that. I don't exercise a ton at all for weight loss, I like the way it makes me feel--strong and empowered.
What made me fat? Overeating high sugar, processed foods, simple carbs (cookies, cheap chocolate, brownies) and laying on the couch feeling sorry for myself. Genetics are not on my side, I have overweight parents, thyroid and hormone issues, but it's also not an excuse.
In the end it doesn't matter to me if it takes my body 2000 calories or 7000 calories to burn fat off my butt. When I feel good about myself, have a good attitude and put good fuel into my body, that = feeling great and changing my body.