Quartus newest version significantly slower than version 9

You can't create a project in Quartus without targeting a specific device, so I'm confused by your first statement, unless you're saying you chose the device family and the option to let Quartus automatically choose a device from that family for you (in the New Project Wizard and Device settings).

But then, are you saying you are only simulating designs and not compiling them? "Compile" means you are synthesizing the designs into logic primitives which then get placed in specific locations in hardware.