Is there a reason that Skinwalkers are limited to 3+1/2 character level shape changes per day?
Since you can stay in the alternate form for an unlimited time, you could just always stay in alternate form. Maybe use a Hat of Human Guise if you want to blend in.
Or, since it starts with a base of 3/day, you could stay in alternate form most of the time, and still should have enough changes switch to human if needed and switch back in dangerous situations.
The Kitsune is a very similar race with no limits on their change shape ability.
For that matter, having an ability modifier tied to changing shape is certainly thematic, but is it necessary? Couldn't they just have their ability modifiers all the time, since they have the normal +2/+2/-2 modifiers.
Again, Kitsune have their ability modifiers in all forms, and with no time limit on shape changes you can remain in alternate form constantly to keep your ability bump.
Is there a balance reason for these limits I am missing?
Not really. I think it mostly revolves around PF's phobia of at-will abilities.
It does bear noting, though, that kitsune get no additional abilities when they change; it's almost 100% cosmetic. Skinwalkers get that choice of claws, darkvision (very useful) or a natural armor bonus.
Actually, you have to look at a Kitsune as the reverse of the Skinwalker.
Kitsune in normal (fox-person) form has a bite attack and full ability scores. They can't use the bite in human form, but retain their ability scores.
Skinwalkers have partial ability scores in human form and no natural attacks. When shape changed, they get full ability scores, and (one of several options).
So is the versatility of the Skinwalkers' Change Shape enough to justify the limitation on times per day? Especially since you could just stay in the shifted form indefinitely unless you want to change your additional ability.
I agree, though a lot of people might get nervous if you're walking around as a werewolf 24-7, depending on the campaign setting. Losing a weak bite attack, though, isn't losing much.
Also, it was recently revealed to me that, since the Kitsune Change Shape explicitly functions like alter self, that means it has to be activated and has a 1 minute/level duration.