They can "limit" based on skills, they can "limit" based on country of origin with the main difference being not using the hot-button word "discrimination" to, err...discriminate between the two while implying some sinister race-based system of visa allocation.
> Maybe we should only discriminate on an individual level and with the attributes that individual has under his control.
They you'd be "discriminating" against people who can't afford advanced degrees from prominent schools who just want to work hard so their children can have a better life like the countless number of first-generation citizens I've met over the years. This is where I'd put a "why you hate poor people?" to make my point but I know that's not what you're arguing.