When I get a new pony that's completely new to me, like I don't have her already, I put her on display regardless of her condition. Then if I happen to come across the exact same pony in a better condition, I take the old one off of my display shelf and put the new one in her place.
I have yet to really get rid of these ponies who aren't in as good of a condition, I have them sitting in a box. I will probably get rid of them at some point, as it doesn't feel quite right having these things put away with no intention to take them out, when someone else could have them instead and maybe they'd actually display them.
For a couple examples, I got a Heart Throb at the Goodwill mixed in with some other ponies. But the poor little thing has what seems to be bite marks in her head! I assume a dog in a previous house she was in got its paws on her at some point. I had her on display for a little bit, more toward the back so her wounds weren't super noticeable. Eventually I happened upon another Heart Throb at an antique mall who was in a much better condition, and put the old Heart Throb away so the new one's taken her spot.
Another example is I have two of the 25th anniversary releases of Butterscotch. The first one I got had some visible marker spots on her, and I had her on display for years. Then just late last month (or early this month?) I found another at Value Village who didn't have any marks on her, and she's now taken the other one's spot on my shelf.
I don't know if I'd ever intentionally seek out ponies in better condition to ones I own, but if I happen to come across a pony that's a double of one I own and is in a better condition, I do get it and put it on display instead.