Interesting points, OutFoxed! I certainly encourage you all to continue the discussion with your opinions, as what you all think is just as important as what I think, but here's how I see it:
Most (if not all) of the disciplines would be geared with the idea of the top-level disciplines; you tend to see thoroughbreds and warmbloods in non-breed specific hunters competitions (with warmbloods usually beating the thoroughbreds due to the specialization of warmbloods and changes in judges preferences recently), but occasionally the odd quarter horse will pop up and do pretty well. Same as in jumpers, dressage, cross-country, etc. -- a lot of horse breeds can excel, but it's kind of a "hard work beats natural talent" that comes into play there. So while a quarter horse might actually beat a warmblood in a couple of show jumping rounds, this won't be the case in at least 90% of high-level competitions.
Am I making sense here? I know I'm restating a lot of what you've said xD
With that being said, if the bonuses were put into place, they would be geared towards the "top-level" shows that take place in real life, but I really like the idea of not implementing them until later levels in showing, just like in real life. I also feel like if they were to be implemented, that would really increase the role of breed associations -- they'd then have incentive to create breed-specific shows, just as in real life -- and that way breeds that wouldn't necessarily be designed for the discipline could still earn prizes and win shows ^^
FEI would probably be the standard for non-breed specific disciplines, just to allow for a general standard that'll be recognized around the world. I figure warmbloods have such success in show jumping because they've got the conformation that allows them to get over the jump cleanly as well -- plenty of breeds could race over the jumps, especially thoroughbreds with steeplechases as an example, but warmbloods have uniquely proven their conformation to be such that they can get over high jumps neatly while not sacrificing speed. I do like that idea for conformation -- a bit more subjective than simply counting up the highest stats, but I like it ^^ Coats and markings could be thrown in there too in order to find a horse with the most ideal type.
I am, however, having difficulty in determining which breeds/types would get which stats, as some breeds simply don't fit into the typical disciplines as their type would, and it could get really complicated really fast if I went by each breed xD
The problem with english pleasure is, again, the accessories -- hunter horses would look exactly like english pleasure horses, and I'd just have to change the stats ever-so-slightly, which would actually be fairly hard to narrow down ^^'
Those are just my thoughts, though. I'd love to hear everyone's opinions on this!