Although I have never used it, but as Xilinx system generator is a Xilinx product so I think ISE needs to be installed.
That being said, ISE is too old. Engineers currently use the Vivado design suite (free web version is available).
If you have Matlab installed in your system, then while installing Vivado (or perhaps ISE also), if you have already chosen the necessary installation options, I think it will install the 'Xilinx system generator' or whatever equivalent of it in Vivado. Just try it out!
you are right ISE is old nut the problem Vivado don't support most our FPGA like Spartan 6 and vivado support only FPGA 7 and higher
About installing vivado, I do that but I didn't recognize any option for installing Matlab system generator (wish Xilinx don't give up this application also like many other application)
I hoped to find a speared file that help to install Xilinx system generator
I would say stick to ISE, since you want to use Spartan6.
Install Matlab with all the components you need FIRST.
Then install ISE and make sure the option for Xilinx system generator is checked during installation.
If the Xilinx side does not detect the Matlab installation, look for ways from the Matlab side to detect the ISE/Xilinx system generator installation.