This sounds like a fairly reasonable suggestion. I don't know if the devs have thought about this option or not, but if they have and they had specific reasons for rejecting it, maybe they can take a second look at those reasons and the contents of this suggestion. It does feel more practical and interesting than current warp gates.
ADDITION: Actually, thinking about it a bit more, the option of a popup menu upon nearing the warp gate doesn't quite work in my head, so I have two ideas that may fix this problem:
Option 1: The warp gate's destination is predetermined from the warp gate module on the station. This basically lets the player choose where the warp gate sends the player, essentially avoiding the issue of having to go through a popup menu every time you want to use the gate.
Option 2: Upon entering the warp gate, the player and ship enter a separate area from the rest of the map that can only be accessed via a warp gate (I imagine it looking something like an infinite loop of the light speed animation from Star Wars). There, the player will be presented with the option of designating a destination from within the ship. Upon selection of a destination, the player will continue to be inside the isolated area for a set amount of time (simulating travel time, much like a system-to-system jump in Elite: Dangerous) during which all players are still able to traverse the ship and do various things, but all systems are essentially deactivated (logic will likely continue to function in order to prevent automatic doors from breaking). Upon completion of the travel time, the player and ship will then re-enter the main map at the designated destination. This one is my preferred method, although it is much more complicated, because it makes the process of warping much more interesting and much less instant, while still being much faster than simply flying or jumping.
