Some more silly and potentially unwanted suggestions. Adding options for a credit cost to use gates. And for ships to get randomly get damaged like hyperstorms or rarely get totaled with d-mods. A tiny chance of ship disappearing, along with whoever is piloting it. Sometime redirect the fleet to another random gate. Or have ship separated from the fleet turn mad and hostile. Because those gates are old and out of maintenance, of course.
I dislike punishing the player for using a feature as intended. I figure that if they installed this mod, they are looking for something a bit cheaty and if there's a downside to using gates, especially after the mod has already been released, then that won't go over well.
Of course these downsides could be turned off via an options config, but optional features add code complexity and also, imo, make a mod seem non-vanilla. I'm not anti-configuration, but if something can be worked into the mod without needing a config option, I'll almost always take that option.
And what you're describing would fit perfectly with Alex's approach to the game with one alteration. Make it so that you can always
use a gate, but if you don't have enough fuel, then bad *** can happen, directly correlated to how much fuel you're lacking.
Not sure about using credits for a gate jump; travel is about managing fuel and supplies. Plus it'd be hard to explain why a gate can use either fuel or credits.