I have an idea for and xpack or a mod where protecting your capital has more use. When it's captured you have to take in back in 10 or 15 turns or so, or take a severe economic and influence penalty and lose 5000bc. Also, to move your capital, you must first: not have the original in enemy hands, and second: you must pay 500bc, then a fleet of 5 ships named bueracratic transports appears above the former capital that must all make it to the new capital. There is a 200bc loss and an economic hit with each one shot down, and (not sure in this but, if they all die you lose because you are on one!)
Also, numbers not 100%, and it would be really cool if, when you get the message telling you to get the world back it said "Congradulations on making it off-world just in time [leadername]!