As long as your son has taken the requisite number of math courses, the fact that these are called "Math Skills" will not be held against him in the strictest sense at many colleges. What I mean by "the strictest sense" is that colleges that require three years of high school math will typically accept the three years that your son has elected.
However, there are some schools that also require that certain topics have been covered during those three years. The University of California system, for instance, demands:
Three years of college-preparatory mathematics that include the topics covered in elementary and advanced algebra and two- and three-dimensional geometry. Approved integrated math courses may be used to fulfill part or all of this requirement.
It's not clear from your question if your son's Math Skills classes are considered remedial, or are they simply "average" as opposed to challenging? Do they cover algebra and geometry--at least on some level--even if they are not actually called, "Algebra," "Geometry," etc.? If they do, then they should fall under the "approved integrated math course" category. If not, then some institutions may not accept this math.
In addition, the more selective colleges will be wary of a student who has been in a lower math sequence throughout high school. Even though this might not be an automatic "deal-breaker" if the student has other strengths that are attractive to the school, it might be something that goes into the "Minus Column" when that student's admission verdict is being weighed. If, however, there's enough other ammunition in the "Plus Column,' then the less challenging math sequence won't ultimately affect admission outcomes.
Bottom line: Depending on the particulars of this math sequence, it may affect your son's acceptance at some colleges, but he should still have many options nonetheless.
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