As one of the few people I personally know that actually like this concept and have repeatedly stated that it's been needed for a long time, I can see people's issues with this, and have my own ideas.
1. Put a delay on communication in this channel. Like a yell a minute or something. That would cut down on people who want to clutter it up with spam and bacon polls and whatever nonsense. And speaking of polls, do not allow polling in this channel.
2. Add a way to report someone for spamming up chats and issue suspensions based on severity. This isn't just for the yell channel. This is for ALL channels. WoW has a report spam feature, and they suggest you use it for people that are being bad in their public channels. Because FFXI wasn't made for the mouse, I think the best would be to add in a command "/reportspam 'name'". This would issue a report to GMs with a timestamp so that they could look at the data and decide what needs to be done. Maybe hire a special person to do just that, because I can only imagine the amount of reports they'll get.
3. I like the above idea of linking the four Port zones and Whitegate together, but I have a feeling they can't do it because of how regions are coded. It's the same reason you can't invite someone from outside of your region.
That's all I got for now.