Overall, it does seem kind of silly that Ethers and such have never been sold at standard Poké Marts, because it is extremely easy to go through an entire game without ever needing to use one. Because it is often so easy to simply go back and heal at a Pokémon Center or with a Doctor or Nurse if your PP starts getting low, and because you typically have six different Pokémon with at least two offensive moves apiece in your party, there really aren't many cases in which having Ethers available for ready purchase would have much of an effect at all. It might help for the Elite Four, but still really isn't that necessary, so I think it would be fine to have them available for purchase in standard shops.
About all it would do is give a little bit of convenience if you didn't want to return to the Pokémon Center as often when training your Pokémon or something, so I certainly wouldn't expect it to be game-breaking to be able to buy them. Full Restores are certainly more useful in practice, and they can be bought.
As for the Master Ball comment, it's completely different - though I do wish it was slightly easier to obtain them/obtain more than one. I never use them in the end, since I don't value any one Pokemon highly enough to use the only one I'll get. If, however, we get given three throughout the game, I'd feel okay using one or two on legendaries and saving the last for emergency situations (like a mid level shiny when I've only got level 100s on me).