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I'm not sure I fully understand - will you have a PC running MATLAB or do you want MATLAB to run on the controller ?
If the former I don't think you need anything like as powerful a controller as you suggest, you can control 12 PWM s and inputs (analogue ?) with a micro clocked at 200MHz or less.
It won't need very much RAM.
If the MATLAB will be running on the controller (and Mathworks offer tools to make this possible) you might do it with a Raspberry Pi but it's IO is limited.
If you want buy ready made kit that will just plug in and go then look to SpeedGoat or DSpace - but expect to spend a lot of money.
If you could explain the task in a bit more detail I might be able to help better.