What about using beams similar to docking? You enter a teleporter block and aim your beam at another teleporter block and it would transport you there. Problem being that you'd have to be able to see the teleporter blocks. Maybe it could be done with something like build mode?
That seems like quite a hassle, the system I suggested would be click and go.
Extension to my previous post - their should be permissions on each block to define who can connect to this teleporter, and if anyone can. So if some one is not a high enough rank, they don't land there, and if they are not in your faction, they dont land at all. There should also be the possiblilty to have horrible consequences from teleporting, such as if 2 people beam out or in to the same pad, they can end up merged some how, and incontrol of the same entity, and require a special process to reverse this, if one goes offline, the person left incontrol would have to fight a randomised sequence of controls from the server, that would make being like this insufferable