Hello,
As some of you might know, I left an issue a while back, specifically #1946 (which is about the inconsistency between BungeeCord servers). I have a suggestion that can fix it: A BungeeCord plugin.

I'm not 100% sure about Bungee plugins, but somehow each Essentials plugin takes commands from the BungeeCord plugin. For instance, let's suppose there's a two-minute cooldown between using /heal. Assuming servers had synced health, you could go to server 1, use /heal, go to server 2, and use /heal successfully again (despite there still being an active cooldown on server 1).

Now, let's assume that the BungeeCord plugin was properly installed and configured. Our player does /heal. This makes Essentials on server 1 tell the Bungee server "Player foo used /heal; cooldown disables at " (but with UUIDs). Then, the Bungee server remembers that. Once foo joins another server, the Bungee server tells that server "Enable heal cooldown for foo until ."

This would also make Essentials banning even better, as the server would just tell the Bungee server Bar banned Foo because 'Demo ban', and then the Bungee server would worry about keeping Foo banned. There might be a config option to send the ban to all servers (although, it shouldn't be necessary, since anyone running Bungee should be using iptables or some other mechanism to keep players from directly joining a server).

Servers could also be grouped, i.e. if you had two synced survival servers, you could preserve the cooldown between servers, but not have it transfer to a creative server.

Broadcast could also be sent to all servers; /tpa could work between servers, etc.

Now, as I said earlier, I have no idea how Bungee plugins work, so I don't know how possible this is.