The whole passage in John 20 is about Christ and His message. That is the message that was taught to the disciples which they in turn shared with the Jews first and then the Gentiles. That is the message that Christ is wanting the disciples to share. It's ALL about Christ and Christ alone.
I agree that Christ wants us to be one. But the problem is that the RCC has departed from the Word and has brought in false teachings such as the papacy which is not in the Bible, equating "tradition" with Scripture, the practice of indulgences, the worship and praying to Mary, Mary remaining a virgin, her assumption, her role in our salvation, whole sections of the RCC devoted to studying Mary instead of Christ, the reversal of doctrines by various popes, the practice of eisegesis verses exegesis,etc.
Eisegesis involves 1) imagination: what idea do I want to present? 2) exploration: what Scripture passage seems to fit with my idea? and 3) application: what does my idea mean? Notice that, in eisegesis, there is no examination of the words of the text or their relationship to each other, no cross-referencing with related passages, and no real desire to understand the actual meaning. Scripture serves only as a prop to the interpreters idea.
Exegesis involves 1) observation: what does the passage say? 2) interpretation: what does the passage mean? 3) correlation: how does the passage relate to the rest of the Bible? and 4) application: how should this passage affect my life?
Read more: http://www.gotquestions.org/exegesis-eisegesis.html#ixzz355tVgfFI
The other common complaint I notice from almost every other adherent thinking their group is correct (and they are legion) is that the Catholic faith differs in many ways from their own and is wrong; well since they were only found five hundred or less years ago in order to rebel against the Orthodox, well yes it differs considerably as one would expect of any new religion, denomination, sect, or cult. They have no legitimate historical claim; only the other Orthodox can make that claim, so they are following something someone formed five hundred years ago or less, frequently far less. Of course they don’t agree with each other either and accountability is ephemeral. Can I mention Bill Gothard ?