Off world colonies are an ongoing problem. I tried to get some code that would make spaceports link you to trade, but it didn't work very well. Later I may go back and try to fix it, but now that I've put in RevDCM, that means I'll have to merge the source code. I'll put a link to the thread here.
http://forums.civfanatics.com/showthread.php?t=316111&page=2 In compensation, I made a couple of buildings that connect He3 to the trade network: one is a National Wonder "He3 Exporter" that requires He3 and a spaceport, and puts another building "He3Importer" in every city, and that building gives its city a Free Bonus of He3. I'll add more buildings that do the same for a few other resources. Its an inelegant solution. And inexplicably He3 occurs VERY rarely.
Units that can found cities: All three kinds of Space Battleships and Space Carriers, Nanoswarms, Workbots, Transhuman Settlers, Colony Ships, Settler, Air Migratiion. Carriers and battleships have this based on the concept of Battlestar Galactica. If you have one of these left you can concievably restart your entire civ, they are so huge. Also, to entice the AI to settle off planet. Nanoswarms and workbots are so versatile and high tech that logically by the time they exist they can build a city, including inhabitants of some sort, from scratch. Settler, Air Migration, and Colony Ship are a progression of settlers with different kinds of transportation. Transhuman settlers just reiterate the point that in the future the "population" represented might consist of more than just standard humans. Also all the extra settlers were partly made specifically to keep older forms from becoming obsolete when one new form becomes available. I don't want you to have to build an expensive colony ship just to make a colony right next door. Since only the Transhuman Settler and 3 tiers of regular settler are pure settler units, the others do not contribute to clutter since they have other functions. Edit: I eventually took settler away from the big spaceships, though all but the first versions of them can upgrade to Colony ship.
The different fuels coming too fast? I don't understand. You have oil, but if you don't have it but have grains you can build a Biofuel factory at a health cost, and/or if you have coal you can build RocketFuel plant. Rocket fuel and varous kinds of batteries (lithium or electrolytes) can allow Highways and some kinds of light armored units, but batteries cannot be used for rockets. Some units can use uranium or lithium for fusion once you have fission and fusion, others eventually use Antimatter etc...Every civ will not have lithium and you cannot make it, but there is a decent chance of it and there are alternatives. Same with uranium. Antimatter is purely manufactured by buildings.
The jumps in raw strength are somewhat mitigated. Most of the advanced units have strong promotions and bonuses that give them relative achilles heels. Transhuman militia has been made a defense only unit. Early hover dreadnoughts move extremely slowly. Hover tanks have a large defensive bonus in cities and are very available. The conqueror drone line are bonused up city attackers that can move very fast on all terrains (other space units, like gunships, generally cannot capture cities). However, Conquerors can be pretty easily killed if caught outside cities or on defense. The idea with them designwise is to make sure they don't have blitz and must work with other units to take cities. Perhaps now that I think about it, I'll try toning down Conqueror raw combat and give them blitz to make them mop ups, leaving spacecraft the big fight. Another thing is the Sentinel which just has pure combat power without a lot of huge bonuses anywhere. Big spaceships can take it out though and let the Conqueror mop it up.