I don't think cross server for WoE is really going to happen. It's not a bad idea and it most likely would be a step in the right direction, but it's not going to happen. It takes a lot of work to make existing servers connect with each other, troubleshoot issues with doing that, and keeping up stability. It would be somewhat a different story if they implemented things like this when the servers launched, but they didn't and who knows how well SE has kept up and modified their server architecture over the years.
I think Insaniac has a great point. There's really nothing of value in WoE anymore and I feel the new merit weaponskills killed what little reason to do them. The drops are too random and the times when people are in them are too sporadic to actually be able to do them.
The only time I do WoE is prime JP time. I do support the idea of making the confluxes scale with the number of people in them. Say, let people go into them and be like a loading zone like limbus. After a time limit let people build up and after the time limit scale the difficulty of the conflux. This way either you could go in with a big group or just random people and still be able to do whatever flux you want. Maybe make the item drops scale with difficulty as well.
On the other hand, SE gave us the tools and means to do the confluxes, it's all on us how to actually do them. They weren't made to be solo and they were made for big groups. How we get those groups is all on us. How do you get anything else done in FFXI? you either shout or make an LS. While I really like the scaling idea, I'm not to optimistic that they would do that. What they should do in the first step is make the drops more worth while. Make the fluxes actually drop things needed. AF seals, elemental stones, and better drops besides crappy logs and things not even worth NPCing. They should increase the rate of coin drops. Now that we can get new weapon skills in like two days worth of meriting there really isn't any reason to do WoE for a random coin drop that you might never see. The time I spent in WoE waiting for a coin drop I could of gotten enough merits to unlock a comparable weapon skill.