I've been thinking about this a lot recently as I like to ride both and I thought I was a weirdo for that (might still be, I dunno!).
I grew up riding natural trails and still love it. Even riding the same route again, it's never the same. You have the personal acheivement (for me anyway) of getting over "that mahoosive hill" put in front of you. You never know whether a drop can be rolled until you try it. The hills can be ridiculously steep and rocky and potentially fatal if you get it wrong. You get trails like Snowden and The Beast (Peak District) which can be just harsh and never designed to be ridden down/up/along!! You also get long stretches of smooth trails and maybe some tarmac for a breather. It's so varied! Fun on a modern full-sus as you can ride for hours and hours without feeling like youve been tumble dried with boulders or you can enjoy pinging off the hillside on a retro fully rigid. All good!
Trail centres ARE like climbing walls, a bit. They take out the "is there a walker around this corner" factor, so you know you can go as fast as you dare without the risk of flattening someone. You know someone isn't (well most of the time) isn't going to riding the opposite way to you either. I've never done a black run I couldn't do and I know unless it says "mandatory air" I'll be able to ride it, so I'm not afraid of trying. I can do sections and sections over and over again to practise something or just repeat the enjoyment! (yeah I know you can do this elsewhere too). There isn't going to be any deep bogs or stiles or gates or anything. I've only ever got to the limits of my modern tyres at a trail centre to be honest (maybe I'm not trying hard enough elsewhere!). And the trails are designed to give the mountain biker, no one else, the maximum fun from the terrain they are on.
I'm not going to go through the negatives of both as I don't care... We don't have to choose trail centres OR natural, we can have both. As long as we all try to maintain good relationships with local landowners and park authorities for the natural stuff, and the forestry commision and all the other bodies who provide the trail centres then we can enjoy the benefits of both for a long time to come.