Having the custom chat channels means that you have a broader impact when you for example need people for a raid or for 6-man groups, and it fosters a better bond between different guilds. It's also a boon for RP-guilds (although I don't think there's many of those left, even though there weren't many of them to begin with) and can help when it comes to open-world PvP-warfare (Members of guild A in Alliance A attacks members from a guild in Alliance B, B-members call for help in Alliance Chat B, who then rallies, which makes members of A call for help, and a massive brawl ensues).
Having people on your friendslist is useful, sure, but you'll have a bigger impact and a more streamlined way of contacting people when you can reach more likeminded people at the same time instead of spamming Global, for example.