So, when or if you were going to do a retirement breeding (and you kept all your lines), would you breed your 2 highest pointed animals even if they are not from your most recent generation? Or would you breed the last 2 animals you trained (so, the newest generation)? 

I'm leaning towards 2 highest pointed animals...

Just depends. 

Live always done most recent gen. But I know some who go for the highest and then train the new gens in more privates. 

Also depends on how many offspring each has?

If I'm restarting lines then two highest pointed animals. I like to start off well. :) But if I'm going to continue on a line, I like to make sure that I'm not going to end up with crossbreeding at the end of a gen if that makes sense.

Considering I just did a ton of retirement breedings to re-start some of my lines, I did a combination of the last ones I trained and the highest pointed match ups. That way I can continue my lines but start off with good points.

I've only done one but I did the top Paints I had at the time. But both mare and stallion had come from the store, so no worry on crossbreeding. 

Paints since 6-8-14

I don't think I'd crossbreed (the game doesn't let you, I think?). I like the combination breeding Kyuubi! 

For my Kabardas, I was wanting to breed my 2 project horses. They are different lines too, so no worries about inbreeding down the line... I'm just unsure about the 5 other breeds I might restart. My real goal is to have higher quality lines and I think on HP people value points more than higher generation.

I fell like you have hit the nail on the head here. HP loves Points. Generations are just an extra bonus.