More launches mean more cost, especially if you're scattering it across launch pads located around the world. There aren't many sites that can handle significant launch masses: Cape Canaveral, Baikonur, Plesetsk, French Guiana, Jiuquan (China), Satish Dhawan (India), and Tanegashima (Japan). So you have enormous coordination between nations that have widely varying launch experience for their heavy lifters, that use different technologies and procedures, and have different goals for their space programs. This doesn't even get into the politics of "What do you do for me if I agree to lift this 15T payload into orbit?"
It also would cost more fuel, since launching from different locations means having to match inclinations. This has already led to one major limitation with the ISS, since its inclination is a compromise between the ideal inclinations for Cape Canaveral and Baikonur.
On top of that, you add complexity in having to dock so many more times, increasing the risk of an incident. While the potential loss from a single large launch is significantly more than that of a single small launch, the cumulative risk of any loss is greater with multiple launches. Putting a thousand tons into orbit would take eight SLS launches, but a minimum of 44 launches of the Delta IV Heavy or Proton, currently the heaviest launchers available.
I would rather see projects like the Falcon XX or MCT encouraged, and I expect they'll be showing up on the test schedule around the same time as the SLS. But NASA is going to have their own path despite the costs, and so they may as well work on an SLS-class launcher. If nothing else, it will give SpaceX (and maybe others) something to aim for and probably provide some valuable lessons along the way.