Lurker described it well - Ballistic is tougher, and will in general last longer, but it's also heavier, less flexible, and in general more 'synthetic-feeling' than Cordura. You'll notice that a bag made of ballistic nylon will feel considerably heavier and less supple than a Cordura bag.
Cordura is MUCH better than standard packcloth nylon, but not as 'hard-core' as ballistic. It's very durable, very solid, and is a solid indicator of quality. I'd never feel bad choosing Cordura.
Either is an excellent material for a bag - it really depends on whether you prefer the more canvas-like look and feel of Cordura, or the slicker, thicker Ballistic.
All things equal, I think ballistic is a better fabric, but not enough better to make it anything other than a choice of personal preference.