In what ways did the Reformation fall short?  

Sam Waldron explains in this video that while generally speaking, the Reformation made significant progress in conforming life to Scripture, there were still certain areas where reforms were incomplete or they did go far enough. These shortcomings still negatively affect the Church today.

For instance, Martin Luther held to the state church doctrine and of infant baptism because they were assumed to be part of the Church. Yet, these two false beliefs were rooted in tradition and not in Scripture. We must continually be reforming and seek to understand how we might conform our lives and beliefs more closely to Scripture. 

Psalm 71:18 (NKJV) – “Now also when I am old and grayheaded, O God, do not forsake me, until I declare Your strength to this generation, Your power to everyone who is to come.”

When you look back at the Reformation and ask if there are ways in which it was incomplete, which it didn't go far enough, in which it didn't reform enough, I do think that there are some things that happen later and that are still affecting the church today that are quite important. I look at them as the natural outgrowth of the principles of the Reformation, but they were not things that were clearly stated and implemented by either Luther or Kelvin and the early what are called the magisterial reformers. And one of the primary areas of reform that I think flows out of the Reformation, but which was not a part of the original Reformation, is the reform with regard to the church and the nature of the church. Luther and in his own way, Calvin, still held the doctrine of a state church. And indeed in the Westminster Confession in its original version, you have a state church doctrine along with that with the notion of infant baptism.

I with many other Reformed Baptists think that infant baptism and the doctrine of a state church are hangovers from medieval points of view that were compromised by the Reformation so that you still had reformed state churches, you still had Lutheran state churches, and in which every child born in that state and that principality was baptized because they they were assumed to be in some sense a part of the church and when you have that happening you have a very clear you have a very clear remnant of a view of the church that originated in the medieval tradition and not the biblical doctrine of the church, which is believers only church and believers only baptism. Now, the doctrines of grace alone, faith alone, Christ alone for salvation, doctrine of scripture alone, gave birth in the 1600s to the particular Baptist, the Reformed Baptist tradition, and I think though that tradition was the natural outgrowth of the Reformed and Puritan point of view, but it took the Reformation further and insisted that the church is not a subset of the state, that the church is composed of believers only, and that church and state must be kept distinct and separate.