If there is only one Church established by Christ, doesn't the Roman Catholic Church have a better "claim" to being one church, since there are no "jurisdictions" and everyone is under the pope under Christ?
How does Orthodoxy understand the idea of "one holy apostolic church" when there are geographical divisions and even some are/were not in communion with one another?
A few random thoughts...
St. Paul said things like "The Church of God in Ephesus" and "The Church of God in Corinth," and so forth, so that from the beginning we can see that there were sort of self-contained Churches, identified according to geographical locations/names, which were in communion through belief and practice and sacraments, and not based on some central administrative person/group/church.
The Orthodox would argue--rightly in my opinion--that the Bible and early Church didn't say that the Church was supposed to be this top-down system in which Christ, acting through one bishop and Church, would guide the rest of the Church. That the early Christians looked to the Roman Church in many cases for support is undeniable. That those same Christians ignored Rome when they didn't like what Rome said is also true.
Temporary breaks in communion are unfortunate, but not uncommon. For example, the 2nd Ecumenical Council had, if I remember correctly, three presidents: Meletius, Gregory, and Nektarios. I believe Rome was out of communion with all of them at various points, and certainly was not much in favor of Meletius, since Rome supported a rival bishop for the throne of Antioch. Eventually Rome came around and accepted the Council, and considered Gregory a saint. In the East all three came to be considered saints, and the East did not wait for (nor particularly care about) whether Rome accepted the Council, or whether Rome was in communion with those involved. Breaks in communion were regrettable, but things didn't come to a grinding halt just because of them, even if it was a break with Rome.