You can't really compare FunnelFlux and ClickFunnels as they're not used for the same thing - but they can be used together.
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Clickfunnels more or less acts as a page builder. You create pages thanks to templates and define the order in which you want them to appear. They have very basic tracking in place, which is unlikely to be enough for a media buyer or affiliate to optimise a campaign properly.
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FunnelFlux on the other hand doesn't have any page building capability, so you need another software to create your landers, but is the Rolls-Royce of tracking and traffic routing.