is that each port is taking (usually sharing with something else) an IRQ. So with two parallel ports, you're using two IRQs. With USB, you're using one IRQ for however many USB devices (up to 127 in theory) are connected.
This isn't usually a grave concern though as current computers can share IRQs fairly well (though it's best to avoid sharing with the graphics card).
There are adapters out that will allow you to connect parallel printers to USB ports, so if you do decide to move to an all USB setup, you may still be able to use your old trusty printers.
Just something to consider.