Hi! First I just wanted to say that I really like B5 mod, and I hope you keep working on it. I haven't downloaded the latest versio, but the one I played jump gates weren't very useful, and I think I read from this thread that you have disabled them all together. I have always been intriqued by the consept of jump gates, not to mention I'm a huge B5 fan. So I was thinking how the jump gate feature could be integrated "back", in the proper and fun way.
CONSEPT
Planets have fixed border's as soon as you colonize them(3x3, 4x4 or depends on size of the system), inside the borders(yours or enemy/neutral) your ships move normal 1=1. Outside borders(deepspace) moving is very slow(to simulatethe need for crew needs, supply&maintenance, and so on), could perhaps take up to 5-10(balance issue really) turns just for one square(could be cut down with new technology). This would make using jump gates useful. Also later on, ships which can form their own jump points, would give interesting strategic gameplay options, and definitive advantage to race which has advanced jump gate technology.
JUMP GATES
Jump gates would actually have to be build inside your borders. Act as space station. In actual would provide jump gate "resource" to the system for trade route access. Same as building harpor or trade port in vanilciv4. Now what comes to attacking jump gates, maybe they could be made invincible or destroying one would cause nuke "area of effect damage" to simulate huge explosion. Also as stated in actual B5 series "war or not, jump gates must go on" thus destroying one would yield negative diplomatic effects you vs. all races. Building jump gates would cost a lot of money, to prevent spamming. Perhaps the time to jump from point-to-point(travel time) could be simulated.
When ship(s) are ordered to do a jump they go to "working stance", same as workers when more than one turn is needed to finish to job, and when done they appear at desired location. Now perhaps the same method of calculation could be used, as the Great Merchant does with trade mission in vanilciv4(how much money you get), to calculate the needed turns. Ships that have to actually use jump gates, should get jump "ability" one square away from gate just to avoid any "collision" issues. Perhaps modified script of "map area damage effect" could be used, to give the jump ability to the ships. There are two ways the ships could enter normal space after jump. A: They appear next to the gate(1 square) at desired location picked by player, in this case it would make most sense if the jump gates could not be move onto by units. B: When ships jumps from gate-to-gate, and upon exit, they act as units off loading from sea transport. Thus forcing player to move them atleast once away from the gate.
EXPLORATION
Exploration could be done with probes.
Idea 1. Probes are one time usable units and are "launched" from star system. The probe acts as a nuke in vanilciv4, you launch it from system and pick a spot inside area of movement, and upon "impact" would simply reveal area around itself. Could add turn delay effect to simulate flight time to target, instead of instantenious effect. PRO: Would force player to colonize in order the explore further. Area of movement could be increased with research. CONS: Would have to build a lots of probes, and could be tedious. 2. Same as the #1 but instead act as fighters in vanilciv4. Return to base after mission. 3. Normal moving probes with promotion that cuts down movement time in deepspace. 4. Later on you could use ships with jump point capability to do blind jumps. This would bring another interesting consept, no need for open borders. You could always enter the borders of another race, but this would lead to negative points added to you vs. them in diplomatics relations, could even lead to war. Probes would not cause this, as they are only probes. Signing actual open borders deal would stop the negative effect from occuring.
COLONIZATION
Colony ships have the same promotion as the probes, thus cutting down deepspace travel time. Colony ships would need to have defence only capabilities because of pirates/barbarians, since manned battleships can't escort them, or if they did the travel time would be extremely long. With advanced jump technology, colony ship could simply form jump point.
MINING/WORKERS
Game would have two kind of workers normal space and deepspace. Normal space workers have long travel times in deepspace, so are not ideal for building mining bases, instead are useful inside your own borders. Deepspace workers could only build mining/refining bases which consumes the unit and act as space stations, but with weak defence capabilities. The mining/refinery would create small culturate border around the station. Also deepspace workers could house 1 or 2 normal workers(like carriers), so that those workers can build the actual extraction facilities needed on the asteroids, or perhaps creating jump gate near the station for easy access. The jump gate could also be needed to actually "ferry" those resources from the refinery to home world.
So here are my thoughts. When I came up with these consepts I always kept in mind, what the civ4 can already do and what I have expirienced personally ingame, so that these features could be integrated without any actually C++ knowledge. Because you have said that, that is not your strong suit

, but so that you could "borrow"(asking from the appropriate people afcourse) scripts from other mods. I understand that you don't really have a lot of time, to work on the mod these days, but I just wanted bring out might thoughts. Perhaps my ideas will sparkle inspiration to some one who is skilled modder, and would be willing to help you. Once again I hope you keep working on this mod as it rocks

. Any questions about my ideas? shoot!
P.S I'm not native english speaker so bear with me. I also tried to be to-the-point, so that things are kept short as possible. May not be nice to the brain, but gets to the point

.