The reason d20 is used so widely is because it is simple, and because it is the system used by the biggest, widest-known pen and paper RPG out there, D&D. Oh, and they basically provided the core system out there free to use as long as you gave them credit. Why reinvent the wheel when there's a wheel right there?
Having played systems both with and without the d20 system, I can say without a doubt that d20 is much simpler and easier to learn than Shadowrun is, especially this newest edition of Shadowrun. Roll 1d20, add your modifier, if you beat X, you succeed. Simple, and to the point. That core mechanic is what allows people to pick up on the basics of the d20 system so easily. Sure, the fine points take time, but the initial barrier to entry is low. Compare that to Shadowrun. Roll xd6, where x is the sum of attribute and skill plus any positive or negative modifiers, see how many 5s and 6s you got. Compare to your limit. Check the number of 1s to make sure bad things don't happen. If your hits beat the threshold/opponent's roll, you win.
Are there limitations to the d20 system? Sure. You can see this in the differences between Mutants and Masterminds and Hero System. One plays like a comic book, while the other is a tactical, gritty game, with a lot of resources to keep track of.
So I hate to break it to you, but for most people, especially people who just want to have a bit of fun, and not put the effort into learning a whole new system since that is like work and they get enough of that at, y'know, work, d20 is simple, easy, and to the point. Plus, they already know how to use it, and there are mods already in place allowing you to do pretty much anything with the system (d20 Future and Mutants and Masterminds being the best examples).