The Hypergates can be activated and connected, or they can be inactive- not connected at any time. Good idea! I see that when NOT connected they are nothing more than an icon in the map. Only when connected to a destination gate would enemies be able to jump in unannounced through your gate. That would make sense too.
Believing this- I do create a military star base at each end but that isn't totally effective since exiting the gate anywhere along it's path makes defeats the logic of being prepared for visitors as well as entering the gate entry and exit points themselves pretty much mute. Why have a gare at all if they are not required for entry and exit? This feature seems to be a work in process and really isn't polished enough to be in the game right now. A great idea if the bugs get worked out.
Until then, my ships will just have to go it the old fashioned way.
This may be an overlooked point, but as Joe noted, you can active-deactivate any points at any time. It's more overhead, but you do have the option to simply turn off a route at the end of your turn, after you have manually moved all of your ships. Next turn, re-enable it only during your moves.
I use a significant number of hyperroutes as I like to play and huge and up maps, and I already redo them as needed.
Usually, I do build a route into the enemy's areas if possible to make my invasions more efficient, so it's my invading fleet that will use it. I guess, in the unlikely case that I've miscalculated the enemy's strength, I can simply turn the route off at the end of my turn until I need it again to avoid the enemy counterattack using my lanes.
If there were a cost or delay to enable or disable these, I could see the problem. For a turn-based game however, I only see an issue with additional micromanagement, rather than a real strategic issue that needs some solution.
