Suggestion:
Add the ability for the simulations to be slightly inaccurate eg. ferrum aerospace is disabled during simulation (if it is installed), some body lift may not be calculated and some random computer errors.
I think this would be a good idea because it means players can't just simulate everything, they have to build some parts of it to do an actual test. For example, they might build just the launcher with dead weight as the test payload to test if it get to orbit. The quality of the simulations could increase as you upgrade the R&D center.
I know there is already the ability to unlock simulation around a certain body by entering it's soi, but I still feel it's too over powered. Even for small orbital missions people don't completely rely on the simulator for testing, real life tests are performed, usually on just a small part of the spacecraft.