You bring up some really good points. I completely agree that money/winning/etc can get in the way of good solid training and riding methods and lots of people have lost sight of what's important. My first thought is, what discipline DOESN'T have this? But really, what hobby/sport/whatever in the world doesn't do it?! How many professional baseball players got caught (or didn't get caught) using steriods to enhance performance? How many people out there get screwed because a charity decided to run itself like a business and care more about how much money they were going to make? Unfortunately it's a part of life. NOT saying it's right. But is baseball bad because people cheat? Are charities a bad idea because people are greedY? No, you try to fix the problems with it and enchance the good.
You're right, a horse doesn't automatically know how to be completely balanced on its own. But... it isn't "natural" for us to ride it at all. Every riding horse out there is spending a lot of energy doing things they don't normally do and probably can't understand the purpose of. But my opinion is that, it's ok. A lot of riding horses out there don't hate life. It's not natural for a horse to go jump a course, but I see jumpers who absolutely love what they do. Sure, there are days when my horse would rather sit in his stall and eat rather then work in the ring. But I spend a lot of time and energy and money making sure he's healthy, and fed, and taken care of. I do my part. He does his. And we're both pretty happy with our deal. For an upper level competition horse, they have to love their job. Dressage is all about being supple, submissive, and moving freely, etc etc. I don't see a dressage horse that hates his job being able to do it well. If being ridden is such a negative experience, horses will show it. (and some of them do)
1) When you pick the horse with the most natural talent, you can use gentler training methods and equipment and 2) the longer a horse has been bred to do a certain thing, the happier they will be doing it.
I disagree with you on both of these statements. While they can be true in certain situations, are definitely not blanket statements.
1. When you pick a horse that has the conformation and personality that is most suitable for your discipline, it CAN be easier to train it because it is easier for the horse to do it's job. But there are grand prix jumpers that are extremely difficult to ride and train but are superb at what they do. Sometimes that boldness and bit of fight in them that make them so successful is also what makes them difficult. And I'm pretty sure they don't use the most gentle of tack. Perhaps it's off topic since you're talking dressage, but I think the same idea applies.
2. Heck no. Conformation and personality on an individual basis. I could care less about breeds, as long as they can do the job I need them to. My old welsh/QH pony that I bought in a pasture for next to nothing has won almost every single dressage class he's ever entered. Sure, there are certain breeds and certain lines that excel in certain disciplines. But I know a very fancy absolutely beautiful 17.2 Oldenburg with nothing but stellar dressage breeding, tons of full siblings that show and win, etc etc.... with no work ethic. I think he'd be happiest being a trail horse.
Just my few thoughts.