Honestly, I really think the tinges of racism that the OP are reacting to might exist. However, the mechanics exist to
help reinforce the setting. And, with the changes to 4th and 5th Edition from earlier, I will say that it is far LESS against
the Orks and Trolls then it used to be. Trolls and Orks, though have a number of issues to deal with in setting.
First is the simple fact that they are, generally, at the bottom of the heap. The are heavily in the Barrens, and frequently
get less then adequate schooling. This latter is for a number of reasons. With Orks, it is because they develop faster.
For Trolls it is because they get BIGGER and STRONGER faster. Someone tries to bully them in school, and they hit
back, accidentally injuring, or even killing the other kid is a much greater possibility. On top of that, you are going to have
parents and teachers and school staff looking at Ork and Troll kids as "troublemakers" since they have such physical
differences. (A side effect of Ork accelerated development, BTW, is that they are trying to learn stuff AFTER the times when
modern developmental psychologists believe it should be learned at, after the brain can best learn it, meaning they will also
have a harder time learning things because of when they are learning them.)
Second, due to the likelihood of them being at the bottom of the heap, they are not going to get the best nutrition. Orks
will be needing to eat more growing up(and competing against their siblings) because they are growing faster then
humans, while trolls will be needing to eat ALOT more because they are growing faster, and are BIGGER. Malnutrition
effects many things, including brain development.
Finally, they have the prejudices of society. Anything they do is going to be looked at through the lens of the Dumb Tusker,
or Stupid Trog. After a point, it might just be easier to give in to those stereotypes then keep trying to buck the system.
However, Orks and Trolls can reach the same average Logic, Intuition, and Charisma as anyone else, and can get
to high ends just as easy. This is because, frankly, the school systems, even the worst, are good at getting most people
to a reasonable point(the mythical Average of 3, and above average of 4), and you are flat out going to develop certain
social skills and reach a certains trength of personality if you interact with people regularly growing up. Now, for a Troll
or Ork to get Logic 6? Yeah they are going to have to work for it, work hard, fight through all those things that are conspiring
to hold them back. Prove to the teachers they are just as good as the humans kids, not hit that kid that was throwing rocks
at them, get better food in the right quantities. It is not just applying themselves in school, it is fighting EVERYTHING in the
dark, dystopian world that is Shadowrun that is trying to keep them down. And, that is why they take Exceptional Attribute
Logic.
Is the mechanic itself racist? No. Does it convey the underlying racism in the setting? Yes. Does it convey that there are
differences between Trolls, Orks,and humans, through multiple factors, that can effect the ability of those groups to learn?
Does it convey that there is, indeed, institutionalized racism in the setting that is there to put down those deemed different?
Yes, yes it does.
I think, ultimately, the issue is that one has to remember that Shadowrun is not our modern world. It is a dystopian world
where if the square peg won't fit into a round hole, they will beat the square peg in until it either forces its way in, or it breaks.
Trolls are the ultimate in Square Pegs, with Orks being only a little less. The world will try its darnedest to make them fit
into what it wants. It will not, like in the real world, try to help them adapt with special schooling or counseling. If they can't
fit into the schooling provided by the private, for-profit corp that is running the schools, well...that corp isn't going to cut into
its bottom line to help them. That sort of bleeding heart crap is expensive!