The wastegate is simply there to control boost pressure and therefore turbo speed. The faster the blades spin, the more boost you get. The factory wastegate is designed for a stock truck, and stock boost pressures. My truck has 76k on it now and I am pretty suspect that the wastegate is not holding the boost pressue it should. An aftermarket version would likely hold the boost to the number I want, not start bleeding off early or simply not make the boost I need for the fuel being injected resulting in high EGTs.
Some of the bigger aftermarket turbo's will make insane boost, but you might not be able to fuel to the point of overspeed/overboost so they do not run a wastegate. There is always the option of a remote mount wastegate on these set-ups too if you do plan to run them hard.
The wastegate allows the use of a smaller turbo with better low end response and better emissions performance without blowing it up on the top end.