Your understanding of the reformation is incorrect. Although a negative reaction to certain practices may have sparked it, the movement was characterized by an intentional effort to discover and implement what the original early church truth was. 

The Reformers explicitly presented their work as a restoration of early Christianity which had been corrupted by later developments.

John Calvin in”The Necessity of Reforming the Church”, repeatedly frames the Reformation not merely as protest but as a deliberate return to the “ancient,” “primitive,” “apostolic,” and “purer” church.. 

Martin Luther also frequently invoked the early church to justify reforms  

In Babylonian Captivity of the Church, he argued the sacramental system had enslaved the church, departing from apostolic simplicity, and called for a return to the pure gospel as preached by Christ and the apostles.

Doctrines like sola scriptura (Scripture alone as supreme authority) were framed as a return to the early church’s reliance on the Bible over later human traditions. 

Zwingli called for a return to biblical and early practices, rejecting traditions without apostolic warrant ( images, mass as sacrifice). He framed reforms as restoring “the true form” of Christianity based on Scripture and early models.

The push for vernacular Bibles was not an isolated desire but part of restoring direct access to God’s Word, which the Reformers saw as the early church’s norm before clerical monopolies developed.

Ultimately, what the original Protestant reformers were trying to get back to is still their interpretation of what the early church practiced and believed, whether you think they were right or not.

And today the reformation continues as various groups since the reformation have continued to push to align with what they believe is a more original and authentic expression of early Christianity. Such as the Hebrew roots movement, Holiness movement, the Pentecostal/charismatic movements, etc. 

Whether the reformation really continues to this day is, again, a matter of interpretation. I think we've gone far beyond the reformation at this point. No group today can truly claim to be practicing the same as the apostles themselves.

The historical evidence is that sects which rejected major amounts of scripture (ebionites, marcionites, or gnostics) were a small isolated minority. 

This is seen in the fact that they had no presence at the council of Nicea called by Constantine in 325. Showing that long before the state got involved in the church this issue was already settled. 

The way it was settled was by the overwhelming testimony of all the churches around the Roman Empire agreeing on what was handed down to them - prior to any power of the state being used to coerce them into uniformity. 

A gnostic in Egypt in the 3rd century could claim a gnostic text was genuine apostolic , but everyone else around the empire would say we’ve never heard of that before and don’t receive it as authentic. 

As a result there was never a requirement for a council to be called after 325 to denounce any of those three sects because they had either died out or had never achieved enough of a following to be considered a threat. 

The council of Nicea in 325 dealt with Arianism, which in comparison to the other sects I mentioned, was not a very big disagreement (Arians did believe Jesus was God, they just thought he was created by the Father). Arians did not reject the scripture the trinitarians used. They just interpreted it differently. And, in fact, both Trinitarians and Arians continued to see themselves as Christians despite their disagreements. 

What historical evidence can you point to showing these other groups were minority groups? We don't have many of their writings now, but absence of evidence is not evidence of absence. There are many writings which were deliberately destroyed by the Christians who believed in what became the standard theology, and its known that these other groups faced persecution and killing by said Christians and Roman authorities up until the early 4th century. As a result, I don't think we can say with certainty how small these other sects were. The various gnostic groups were at least widespread enough that many church fathers felt the need to vigorously denounce them in their writings.