Absolutely. That's a major part of what we're working on. The Zynq, specifically, allows for this more than has been possible previously. When your ARM(s) and your programmable logic are on the same wafer, you can kick tasks over more quickly. And shared resources are a big boon. This obviously is a gross oversimplification, and not straightforward from a x86 development point of view. The ARM runs Linux, or you can roll your own bare-metal OS for your application, and it plays the role you mention.
