A formal alliance system would actually be cool as hell. This was done in... was it maplestory, or tera? I can't remember. In either case, how it worked was like... let's say you have FC1 and FC2. They both have totally separate members, let's say they each have like 40 players in them. FC1 really likes Gundam, while FC2 really likes Death Note, but both FCs love anime in general. They have a common bond but they're different enough to warrant being in different free companies. However, they're not enemies; they want to talk to each other. So FC1 forms an alliance with FC2, and now there's an "alliance" chat channel where FC1 and FC2 can communicate without leaving their free company or making a separate linkshell or god forbid a lower-member-capacity CWLS if Fc1 is on a different world than fc2. Megachannels like these would only be a boon because you'd get the actual UI benefits of an FC (last login date REALLY helps when you have to prune members; motd is also helpful for getting messages to players who are offline, and FCs in general just have large member caps) while being able to easily chat with people in other FCs. In the game I played where this was implemented, we saw a surge in actual conversation because people could stay in their guild with their pretty guild logo/emblem and their friends while also talking to people in another similar guild with ease.
The game should have a buddy chat too. Maplestory had something like this. It was just a chat channel where, when you typed in it, the message was seen by all of the people on your friends list who had the buddy chat enabled. This did lead to some issues where, say, tim sends a message to jan and I'm friends with tim but not friends with jan so I only see one side of the communication since I can't read Jan's replies. But you didn't really use it for 1 on 1 convos; you'd use it as like, an easy way to tell your whole friends list that you were about to run content and invite people enmasse. Under the current system, to accomplish this I'd need to either add everyone on my friends list to a series of CWLSes and Linkshells (I actually kind of do this and even this isn't feasible since CWLSes have small member caps and I can't fit everyone in them; but nevertheless when I want to do content I will literally spam like 5 CWLSes), or send /tells to like 100 people individually. Speaking as someone who uses the available tools: this ain't it.
Also while we're here asking for QoL chat functions, can linkshells and cwls get an optional "X has signed in" message? People could opt out of it if they want to be incognito but it's NICE being able to say hello to people when they log in and outside of FCs this isn't possible unless you keep your buddy list open and you refresh it constantly like a psychopath.