Nah, the problem is that for some reason builded Way Gates don't have Way Gate ability even when you manually add it via triggers -> it always returns its level as 0. Those Way Gates that are pre-placed in map retain that ability.
So unless anybody more experienced knows how to handle this, you may end up using/scripting custom teleportation system.
That's why I said use JASS code to make locations.
He's got two Waygates that are linked to each other, they'll have two locations each. Location A, B, C, and D. These were all created via custom code.
He brings units to Location A, and they are teleported to Location D. He brings units to Location C, and they are teleported (Moved Instantly to Location) to Location B.
Again, using Custom Code so these locations can be played on the map while playing the map.
That's how I figured this could be done, anyway. xD
As for the visual effect of the Waygate, not sure.
BTW, I think WayGates don't work when they are built is because they're not linked to any location. When you place a Waygate on the map, you have to check "Waygate Active" for it, then choose the Location it teleports to. That's probably why buildable ones don't work.