There are many weaknesses in the IRC-protocol, particularly that every server admin efficiently is a superuser in the network. This was probably the root cause of the bit split between IRCNet and EFNet. The total amount of IRC users continued climbing after the split, but the percentage of total Internet users using IRC started falling rapidly after this. Then we got commercial silos ... it's terrible, like I have 5-6 different chat applications on my telephone, many of them connected to chat networks that are unavailable from the laptop, and yet I cannot even connect to my wife even as she's at completely different chat networks than me... :-(
Anyone can run their own IRCd server/network, if superusers was a concern, the code is open source. Also, many users migrated from EFNet to LinkNET because it had native SSL, very much appreciated for security. Later on, a Blowfish client addon became another option for encryption regardless if the server was using SSL or not.
Today it's not so much a problem, as all IRC clients easily can connect to as many servers/network as necessary - but we're dropping the "relay" part and "network" part if everyone is supposed to run their own standalone server or their own small network.
Back in 1996 it was a also a huge practical problem for the end-users as (almost?) all client software assumed there should be one and only one IRC network, after the split one had to choose what network to connect to. Being connected to both was of course physically possible, but impractical.
In a perfect network topology, there shouldn't be such a great difference between clients and servers - everyone should be able to connect to the network and relaying messages. As said, with IRC every server administrator efficiently was a super user. This meant it was non-trivial to add new servers - every new server and server admin would need to be approved and vetted by the community. That's the reason why they had to throw out the Eris server - it was too liberal on whom was allowed to connect as a server.