Between the two I'd recommend the Arty without hesitation.
The Parallella is intended as a demonstration board for the Epiphany SOC. The $99 model has no GPIOs or JTAG interface, making it essentially unusable for FPGA development; the higher-end models will still be awkward to work with.
The Arty is intended for FPGA development, and is much better suited for it -- built-in JTAG controller, lots of GPIOs on easily accessible connectors, user I/Os, etc.
The Parallella is intended as a demonstration board for the Epiphany SOC. The $99 model has no GPIOs or JTAG interface, making it essentially unusable for FPGA development; the higher-end models will still be awkward to work with.
The Arty is intended for FPGA development, and is much better suited for it -- built-in JTAG controller, lots of GPIOs on easily accessible connectors, user I/Os, etc.