One advantage of it is that it is so obviously desirable. It's difficult to imagine anyone rejecting this value. It is universally applicable: no matter your personal values or goals in life, substantive freedom will help you achieve them.
Negative freedom, or freedom from coercive interference, is similarly desirable, though more weakly so. Substantive freedom includes and builds upon negative freedom. There are different sorts of constraints that may impede us in our life pursuits. There are things that get in our way ("positive" constraints) and needed things that we lack ("negative" constraints). These may be "internal" to our selves, or else concerning the "external" world. They may be traceable back to the agency of other humans, or not. But whatever their nature and origin, the result is the same: an obstruction to our endeavours in life. We should like to overcome as many such obstacles as possible. Negative freedom has value in that it protects us against positive external constraints that originate from the agency of others. But clearly that is just one part of the picture, and substantive freedom will require us to take a broader perspective, recognizing - and hopefully alleviating - the other obstacles that hamper us in the pursuit of our goals.
Sometimes goals will conflict, of course. Your freedom to shoot a gun where you please will conflict with my freedom to not get shot. Such conflicts might be resolved in a utilitarian manner, so that the strongest preferences of the most people can be satisfied. Such trade-offs are unavoidable - even for the negative libertarian.
One possible challenge here could come from the naive utilitarian, who asks why we shouldn't just aim to maximize utility directly. Here I employ the standard response that utility is better served through indirect means. For one thing, on a subjectivist account of well-being, coercive moral paternalism can prove self-defeating. We might hold that autonomy and self-direction is an essential feature of the well-lived life. Further, as J.S. Mill famously argued, there are good instrumental reasons to favour liberty. Individuals tend to be more motivated to look out for their own best interests, and they are in a privileged position with respect to knowing just what those interests are. All of this suggests that the best way to promote human welfare is through enabling humanity. Help people become better educated, well-informed, and generally able to achieve their goals, and then let them take care of the rest for themselves.
So what are the political implications of taking substantive freedom as our core politico-moral value? I previously suggested:
It is not enough to leave poor children alone: by letting them starve, we do not thereby make them "free" in any worthwhile sense. The fulfilment of basic needs is a prerequisite to any form of freedom worth having. And, on top of that, education and parental love are necessary to a child's development into a fully autonomous and flourishing human being. (And, again, this is surely what matters.) Granted, the state cannot provide parental love - though it might help enable it, through family support and provisions for parental leave [from work], etc.
I have other recent posts which argue in more detail that instituting an unconditional basic income, to supplement the market economy, would have extremely beneficial consequences for substantive freedom. But the first step is for us to agree in principle, that society should aim to enable its members. Then we can turn to the empirical question of how best to achieve this goal.