Diotrephes sounds like an extreme case, actually casting brothers out of the church, but Matthew 18:15-17 gives pretty clear guidance on how to deal with someone who is sinning, including sinning in a way that destroys the fellowship and unity within a church. At some point he is cast out and perhaps goes on to start a 33,001st Christian denomination to add to the 33,000 that already exist! (33,000 is a popularly cited figure, but your mileage may vary.)
I don't read 3 John 1:9 as suggesting that Diotrephes' desire for "preeminence" was the problem. The problems were the actions he took, perhaps motivated by a belief that he was preeminent. The typical church structure with a pastor, assistant pastor, music leader, youth leader and deacons makes some individuals "preeminent" to some degree, so this in and of itself is not a hindrance to fellowship and unity. It sounds as though Diotrephes was more of a usurper.
But let's cut to the chase: "What causes fights and quarrels among you? Don’t they come from your desires that battle within you?" James 4:1 (NASB, emphasis added). There is no fellowship and unity within Christendom - never has been, never will be. There are tens of thousands of denominations and hundreds of thousand of churches, all rife with internal and external fussing and feuding, because everyone has his or her own idea as to what constitutes "Christianity" and what constitutes "fellowship and unity." The fussing and feuding is largely just a manifestation of the egotistic and selfish desires battling within the individual believers, all of whom want to point to the others as the problem.
This is indeed a puzzling state of affairs, especially if the Holy Spirit is uniquely at work within Christianity. Since there is such a lack of fellowship and unity, most Christians take the easy way out: The Holy Spirit is at work within their lives/churches/denominations, they say - but not those other lives/churches/denominations, who lack "correct understanding," preach "false doctrine" and engage in "ungodly practices."
When someone asks, "Why can't we have more Christian fellowship and unity in this church, in this denomination, on this forum?" all they ever really mean is either (1) "Why can't we at least pretend to be nicer?" or (2) "Why doesn't everyone just admit I'm right about everything and get in line behind me?" Diotrophes is always the "other guy," not me.