My reasoning that the Wish spell would give ranks in a skill is based upon it's effects upon the ability "Inteligence."
I'm not certain about this next bit, but here's what I've been going by so far.
If you use Wish to add a +5 to Strength then it's as if you gained a permanent buff of +5 that can't be dispelled or taken away and you are able to use normal buff spells or equipment with buffs on them to raise the ability by another +5. These buffs however, can be taken away.
Ditto for Dexterity.
Ditto for Constitution.
Charisma.
All of these gain their bonuses and those bonuses don't have any affect on what you did in the past. Even Constitution when raised backtracks over your past as a reference to raise your hp.
But not Intelligence.
If you raise Intelligence later in the game, you don't get skill points retroactively like you gain hp.
If you raise your intelligence using a buff spell or magic item before you level, you don't gain skill points for those points in Intelligence the buffing gives.
Granted, some DM's rule that if you've had a bonus to your Intelligence for more than a certain percent of the time it took you to level then you do gain those skill points, but by the rules as written (Hey, I just got that. (RAW.)) these method's don't give skill points when you level.
This means that Wish gives more than just a buff to stats that you can build on top of.
Now let's look at skills.
As far as I can tell, skills have three stages. Unusable, Untrained, and Trained.
If a skill is Unusable, then you can't use it. (Duh. But a single rank in the skill makes it Trained)
If a skill is Untrained, then you can only use it against DC checks of 10 or under. And a single rank in the skill makes it Trained.
If a skill is Trained, then the DC against which you roll is unlimited. Especially if it's on a project where your DM rules that you can have hundreds of hired workers using "Aid Another" to give you access to truly high DC rolls. (How many people can work on building a tank or battleship?)
Wish gives nothing more an irremovable bonus to a skill which you won't even be able to use until you put at least 1 skill rank in it?
Wish merely raises the skill into the Untrained category?
Or Wish gives an inherent bonus to the skill which is considered a rank or number of ranks and changes it to Trained.
I say that while skills can have a big impact on what you're capable of doing in-game, even more in a number of ways than an ability, it doesn't have the same level of wide spread application as ability scores.
And if you're worried about myself or others using this argument to claim you should also be able to Wish for Feats, remember that skills, like abilities are right there on the character sheet. Not separated from it like Feats are.