Substantive freedom is the capability of a person to choose life form one has reason to value. Or put it differently, substantive freedom is the capability of a person to choose various lifestyle that she has reason to value. Maximising substantive freedom serves as the foundation for Amartya Sen's theory of justice. Injustice, thus, is unfreedom that restricts a person from choosing life form that she has reason to value.
For example, a rich man who fasts to give his meal to a poor man is in a different condition than a poor man who fasts because he has nothing to eat. The rich man here has freedom to eat or not to eat; whereas the poor man does not have that freedom. For Sen, justice would then mean providing mechanism/opportunity so that the poor man too would have the kind of freedom like the rich man.
His book Development as Freedom has very useful practical means to enhance justice. He argues for democracy, not least because democracy as opposed to totalitarian regime is good in itself but because such political arrangement compels political leaders to be accountable to the people. He also argues for the upliftment of women and importance of public reasoning. All such implications are important features he cogently argued for.
One of the flaws, I see, in setting substantive freedom as the foundation for theory of justice is that those individuals who cannot make choices are not included in the scope of the theory. There are human persons because of sickness or from birth who cannot make choices. But since they are also human person, one needs to be inclusive and not just bracketed them out. Thus for a theory of justice to be viable one must have an intellectually robust viewpoint of who a human person is. John Rawls in the opening page of his book A Theory of Justice underlines that each person possesses an inviolability founded on justice that even the welfare of society as a whole cannot orveride. The problem with Sen's theory is that once there is an intellectual loophole, the next generation will live it out in flesh: bad or good. And I fear Prof. Sen does not intellectually protect that flank which a mad political leader or a scientist can perform some bizarre act on those who cannot make choices.
But I must mention that I have high respect for Prof. Sen specially the kind of humility and sincerity he exercises in putting forth his arguments. His books have sharpen my thinking in many respects.