PWM ports on the aquaero allow you to control PWM pumps & fans directly, and it has 2 flow sensor input ports, and 8 temperature sensor ports.
It is possible to setup the aquaero, without USB, using the on-screen buttons, or an infrared controller, but that can be a pain in the butt.
You may want to setup the aquaero, and peripheral gear, while connected to a windows 8 (or higher) system, and then move the gear to your existing system to run autonomously.
There are some peripherals that have the aquabus available, which does not require USB 2.0
I believe the aquaero 4 is retired and is not supported by current software.