So right now, we have a weird mechanic in the game: Every pokemon caught is worth 100 stardust (or 300 or 500 for evolutions). No matter how high its CP was or how difficult it was to catch. This makes for a weird idea in the game: High CP pokemon are less desirable than low CP pokemon. Obviously that makes no sense, but since you're not being rewarded for catching a level 30 murkrow over catching a level 1 pidgey, i usually just don't bother with the difficult to catch pokemon.
So what if instead of getting a flat amount of stardust per catch, the stardust would actually range between 50 and 200 per catch? That way, catching a high level pokemon would still actually be worth your effort.
Seems like an easy enough change to implement as well.