I tend to be a bit wonky with Wishes in my games. First of all, such a spell can automatically accomplish anything specifically listed under the spell description. If a player wants to get something that is NOT on that list, he is walking into unknown territory. Characters using a Wish will ALWAYS get something out of it, regardless of how outlandish the request is. However, the more outlandish the request is (in relation to the "allowed" list in the PHB), the more unpredictable side effects may be. A lot of this has to do with my game's cosmology and "where Wishes come from."
That said;
Wishes for turning a cross-class skill into a class skill? Absolutely. It has relatively little impact on the game or mechanics; it simply lets the character add a little depth to the character.
Wishes for extra feats? Nope. Well, you CAN in my games, just realize that there will be a side effect. Nothing to allow me to be spiteful; rather a side effect that will, at the same time, place some sort of inconvenience on your character AND advance related stories and plotlines.
Wishes for extra skill points? Yes; following the similar rule for allowing up to a +5 enhancement to an ability score, I allow for up to 3 additional skill points per level. They are, of course, not retroactive.