I have a few thoughts on this. First, if you are going to keep the horse forever, no matter what, then who am I to tell you what to do?
I, personally, would not breed a horse like you describe. I think it is nice that you are putting thought into it, btw. I can always find a sweet lovable horse that has a few conformation quirks and isn’t going to the Olympics in a low price range. Heck, Ive found ones with nice conformation (just a bit green) when you open it up to mixed bloodlines. They are also ready to ride (i.e. you don’t have 3-4 years of expense first). I’ve done this many, many times. Breeding one would be WAY more expensive and you may also spend a load of money and have nothing to show for it (as you know from the previous foals). Bad things happen. Weigh the risk vs. reward.
Second, I strongly believe you breed an animal that will contribute to the breed and/or sport (personal feelings on breeding anything).
Third, just because she is a sweatheart doesn’t mean the foal will be. Some of the nasty horses in this world came from sweet moms. For example, you can even have full siblings and have quite different personalities. I’m not saying you won’t usually get a sweatheart, but there are no guarantees. So take her limitations and then add the possiblity of a sullen, or lazy, spooky, or whatever attitude that isn’t a match to mom’s. Now what? Don’t count on the stallion to fix that neck or leg length. It’s nice when that happens, but I would never count on that. Also, are you comfortable with the risks to breeding your heart-horse?
So those are my thoughts on breeding in general, BUT in the end, she is your horse and I believe in the right to do what you want, so long as you take responsiblity for the outcome.