I also thought that was a good way to start fresh, without doing a hard reboot and ignoring what came before, and without feeling like a shoehorned cameo from an original cast member for the sake of it, as sooooooo many reboots do. Either way, there's just no way you can reboot something so big without pissing people off, but all things considered, I think they achieved about best case there.
I just had a few problems with their execution in that one, especially a lot of the material they cut that gave a lot of important context and exposition that I feel was important to the story. They were small, but important details, and it showed that there was more focus on explosions and action than on character depth and plot cohesion. Overall I did think ST11 was a strong action movie though.
I had a lot more issues with Into Darkness though, even putting aside the Khan thing.