Unfortunately it's not that easy.. The idea of reusing soil is based on organic growing or no till growing. If you were feeding the previous plant a nutrient line, I would definitely flush that soil before I reuse it. If you were growing organic or no till, then I would agree that adding recharge and other inoculates like bokashi, is all you really need to do. Same concept with the roots. This is the difference between no till and regular organic growing. With no till, you do not disturb the soil, thus the name. You chop a plant or crop, and just add new seeds or clones in their
place. Roots, like all plant life, is biodegradable. Leaving the roots in place has many benefits, mainly being that they release nutrients as they are broken down. But now that you've already broken up the soil, it won't hurt to take out the root ball and bigger chunks.. It also won't hurt to leave them in.