Yes. I would rather say that in English. I don't really imagine a situation where I would use the Norwegian sentence when it concerns apples. A dress maybe, but apples I would rather say: 'Hvilket eple vil du ha?' or 'Hvilket eple velger du?'. 'Hvilket eple vil du velge?' means to me something that will happen in the future, not when you are standing with a friend next to some apples in a kitchen.
In real life situations it's almost always apparent from the context, so it's not as much of an issue as it might seem like.
We also have other ways of expressing both future and desire in Norwegian, so natives will often default to those if they feel like the sentence would otherwise be too ambiguous - thus circumventing the whole issue. You'll learn to do the same as you progress. :)