The following is an excerpt from the Metroplitan's very important "Intervention and Text to the Meeting of the Hierarchy of the Church of Greece (November, 2016)," which can be foundhere in Greek and here in English.
Unfortunately, during the "Council of Crete" some supported the idea that St. Mark of Ephesus (as well as the Council of 1484, which condemned the Council of Ferrara-Florence, and the Encyclical letter of the Patriarchs of the East in 1848) employed the word "Church" for Western Christians. This is not actually true, so I will make a brief presentation on this
St. Mark of Ephesus
St. Mark of Ephesus wrote a letter to the Pope before the start of the dialogue expressing his sincere disposition for dialogue, which demonstrates his good-will, expressing also the will of the entire delegation of the Church of Constantinople. One cannot enter in dialogue and dispute and insult the other side. However, when he realized the whole mentality of the representatives of the Latins, he expressed himself accordingly. Thus, St. Mark was courteous and a Confessor.
There have been important works presenting the life and theology of St. Mark of Ephesus. I highlight two of these, one by Irenaeus Bulovic (now Bishop of Backa) with the title: "The mystery of the distinction of the divine essence and divine energy in the Holy Trinity according to Saint Mark of Ephesus” and another by Fr. Dimitrios Keskinis titled "The Pneumatology of St. Mark bishop of Ephesus and its timeliness". Also, there is the doctoral thesis of Hercules Rerakis on St. Mark’s brother, John Evgenikos, titled "Dialogue of East and West for the union of the Churches in the 15th century according to John Evgenikos."
Reading carefully these three theses one gets to know the whole atmosphere prevailing at that time, and also the Orthodox patristic theology of St. Mark of Ephesus. I underline some points in particular.
First, St. Mark of Ephesus was a great theologian, bearer of St. Gregory Palamas’ teaching, whom he expressed wonderfully.
Second, still as a layman, before becoming a Cleric, he was inspired with the desire of the Union of East and West, and he was preparing with passion and zeal for this task. And while he began with longing for union, he was gradually overtaken by "the disappointment of the theological impasse."
Third, the relevant letter written by St. Mark to be given to Pope Eugene IV, in which there are some phrases for the divided body of the Church etc., was written at the instigation of Cardinal Julian and with great reluctance by the saint, with a view to a good outcome of the discussion. But Julian was not enthusiastic about the contents of the letter, because it pronounced the Pope as the cause of the schism by the addition of filioque, and rather than giving it to the Pope, he gave it to the Emperor, who became angry and banned henceforth communication between the Hierarchs and the Latins, and it was only through the intervention of the Metropolitan of Nicaea that St. Mark was not punished. In no case was this letter read in front of the Synod.
Fourth, St. Mark expressed the whole theology of the Ecumenical Councils, the terms of which he knew well, he limited the discussion to these terms from the beginning, and brought great embarrassment to the Latins, so the theological dialogue that started in Ferrara reached deadlock and the Synod had to move to Florence.
Fifth, the Orthodox representatives, including St. Mark, faced pressures and threats and deception and fraud. Indeed, John Evgenikos writes that we suffered a lot, not only because of the current and upcoming ills, "but also of the lack of freedom because we were restrained like slaves." He also speaks about the long-term deprivation of necessities, about “poverty” and “famine”.
Sixth, during the Council, St. Mark of Ephesus fought for unity with love, he submitted proposals that were not accepted, he struggled and remained tranquil. He had a sincere willingness to seek the truth. And after the Council his "polemics" "were mainly directed to his Latin-minded compatriots, rather than the Latin papists."
Professor Ioannis Karmiris using views of the historians who were present at the Council of Ferrara-Florence, writes that St. Mark considered the Latins as heretics during the Council, too.
"In Florence, too, Mark Evgenikos said to the Orthodox delegates, ‘that the Latins are not only schismatics but heretics as well; and our Church kept this in secret for our nation was much weaker than theirs’ (J. Harduin, Acta Consiliorum, Parisiis 1715 Eq.), and ‘(those before us) did not wish to proclaim the Latins as heretics, looking forward to their return and negotiating their friendship’ (S. Syropuli, Vera historia unionis non verae, 9,5. p. 256).” 
According to the Acts and memoirs of the Ferrara-Florence Council, St. Mark of Ephesus always considered the Latins as heretics and he said so to the Orthodox delegation, but the delegation of the Orthodox Church did not want to express it publicly because of the difficult conditions of the time and as an expression of friendship, hoping for their return.
But, of course, St. Mark of Ephesus after that Council, when he saw the actual attitude of the Latins, expressed himself in harsh terms. He sent the well-known letter to the "Orthodox Christians everywhere across the land and the islands".
This letter begins with the phrase: "Those who kept us in dismal captivity and wished to draw us towards the Babylon of Latin morals and doctrines, but they did not manage to achieve this......".  He considers that he went to the Babylon of Latin customs and doctrines and that even during the Council they were taken as hostages. Elsewhere in the letter he writes: "as heretics we turned away from them, and for this reason we separated ourselves from them.... they are heretics therefore, and as heretics we cut them off".  Latins are heretics.
Those who seek to lie midway between the Orthodox Church and the Latins, that is, those who "follow the middle path", who praise some Latin customs and doctrines, and praise some others yet do not accept them, and do not praise some others at all, and who behaved almost like modern ecumenists, he calls "Greco-Latins" and recommends: "We must flee from them as one flees from a snake or from them [the Latins] themselves; as they are much more dangerous, being Christ-profiteers and Christ-merchants". And later on he writes about them: "Brothers, depart from them and from communion with them; they are false apostles, deceitful workers, disguising themselves as Apostles of Christ".
Professor Ioannis Karmiris observes:
"Because of the above doctrinal differences and deviations of the Latins ‘from the correct faith ... and everything concerning the theology of the Holy Spirit,’ Mark Evgenikos characterizes them as heretics, verifying that the Orthodox Church during that time and possibly since the time of the Crusades considered indeed the Latins not only as schismatics, but as heretics as well, accepting those of them who came to Orthodoxy through chrismation with holy chrism, thus classing them with the Arians, Macedonians, Sabbatians, Novatianists and other heretics of the fourth century according to the 7th canon of 2nd Ecumenical Council, which he recalls in addition to the 16th Query of Theodore Balsamon ". 
St. Mark Evgenikos after the Council of Ferrara-Florence in 1438-39 and after what he saw there, no longer speaks of the Western Church nor even of a heterodox Church; he speaks about Latins and heretics. It is strange that some people involve St. Mark in an ecumenistic mentality and do not understand correctly, first, his courteous attitude before the Council, for the benefit of the Church and of the expected union, while expressing the entire delegation, and, secondly, the Orthodox treatment of the heretic Latins after this pseudo-Council.
Therefore, the selective and misinterpretative mentality of some modern theologians and clergy toward the Orthodox stance of St. Mark Evgenikos in Ferrara-Florence is unacceptable by any means, and when it is used by scholars it is unscientific. Fr. Dimitrios Keskinis writes: “a fragmentary approach, which unfortunately was cultivated either intentionally by western ‘scholars’ or naively by semi-educated Orthodox diminishes this great theologian of the Church and indeed offends our Orthodox conscience." 
See original Greek version for footnotes.