This seems like a nice idea for a mod. Here, I'll dump some ideas.
First of all, the player could first, to start off, make a small ''shuttle'' that uses Electric-jetpack ion drive technology to move the shuttle into a new dimension; Space. This is done by flying above Y=300, and triggers the movement to Space.
Space is an empty place. Once the player leaves Minecraftia, and goes to Space, they can look down to see Minecraftia. Minecraftia is at 0,-something,0. If the player drops below Y=-16, and X is between +100 and -100, and Z is between +100 and -100, the player goes back to Minecraftia. There are also stars, and one nearby that Minecraftia orbits (actually its just there for aesthetics). The rest are rendered like night, but standing still.
There would be 3 major things in space: Planets, Asteroids, and Ships.
-Planets are visited similar to returning to the Minecraftia, but the X and Z bounds are different, to need the player to be within a 200x200 square above the planet elsewhere in space. Upon entering, they go to the planet. Some contain no life, some contain basic life, some contain simple NPCs (villagers or savages, sometimes an empire here and there, with castles), intelligent life (better NPCs than simple ones; they have technology resembling that of the cold war, and usually treat you as a nuclear ICBM or an alien invader who wants to destroy the world and take everything), and advanced life (About as advanced as the Gregtower, but an entire world of it. They detect you and will find and kill you, and the chances of not being killed are slim, unless you have good skills and armour and etc.. Even if you get past security, they will hunt you, and as soon as you leave, they will probably pursue you to get your resources and destroy all of Minecraftia.) Worlds have some different ores than Minecraftia, and each one has different ratios. Some planets are completely uninhabitable, kinda like Neptune, but may have oceans of molten metal/diamond, that can be used for all kinds of HAYO! stuff.
-Asteroids are simply large clumps of different space-rock, with different ores in the rock. There are many types of space rocks, and they can be made into dust, centrifuged and electrolyzed to get resources. The ores in asteroids resemble the rock that makes up the asteroid, except that they have the ore lines/texture visible over the rock texture. Sometimes you may find an abandoned base, with some cool stuff. And sometimes, you may encounter a Zombie Astronaut in the bases, or a bunch of them. And they are hostile.
-Ships are large ''ships'', are mobile (can move) via controls on the inside, or by the AI of the NPC(s) controlling the ship(s). Sometimes, you may find an abandoned ship, that you can raid and/or take. Ships can only move in space, and they can not move above +300 Y or below 0 Y. They also have waypoints for some planets, in the control station/control hub/whatever, and the ones revealed are always random. But, the Minecraftia is always present on the ''radar''. Ships of more advanced races may have NPCs that greet you and help you and etc., while others are hostile and try to kill you. Usually, most low-tech NPCs will be violent and try to kill you, for fear that they will be destroyed if you are not burned to a crisp - in contrast, more advanced NPCs are more helpful and greeting, because they know that if you do anything hostile, they can crispifry you out of existence by only pressing a few buttons or saying a command to a computer.
The player should be able to dock their shuttle in a ship IF its bay is open (if it is abandoned, it may require exiting the shuttle, going to an airlock, releasing it, going in, closing it, and proceeding to power-up the ship and open the bay, when you go back to your shuttle and dock it in the ship). Also, the player can move around inside the ship.
I recommend that you don't make ships large, as they would have to be entities, and entities cause lag when they are huge and/or have several thousand pixels/faces.
Another cool thing would be a planet defense system, using entity or block-based beam/laser/phaser weapons, as asteroids that are just above/near Minecraftia (or anywhere, but putting it near or around minecraftia or another planet makes sense). The player can craft the weapons, and use a shuttle or a ship to deploy them, where they stay static until they are taken back up or destroyed. They require EU to work, and thus need an IDSU in their recipe, because cables + space = spaghettish nightmare of doom. These weapons will only attack a ship if it attacks the player ship/shuttle or an ally ship/shuttle. (this may even bring the implementation of space-factions, even player-based ones consisting of NPCs and/or other players - which would also be awesome!). Another defense weapon, uses TGBMs (TransGalactic Ballistic Missiles) to destroy ships/faction bases/areas specified on planets. Also a deployable weapon, but it needs ammo and EU to operate. Ammo can be supplied by micro-shuttles, that ship ammo from the control hub, to the weapons. The control hub is another deployed structure that uses EU to use/control lasers/missile launchers/micro-shuttles full of TGBMs.
Maybe even there could be probes, with sub-space radar and warp-drives, that are launched off into space in search of planets or asteroids.
Another minor idea, would be Entropic Sludge. It appears on uninhabited planets, kinda like Venus, but the atmosphere is/was tainted by some race that once lived there. The Entropic Sludge is in place of oceans/ponds, and litters the place. It is a useless liquid, but can be put into Reinforced Buckets and dumped out. There is also a chance that, every so often, Entropic Sludge Worms will spawn in the sludge, and swim in it. They only attack something if it comes into the sludge, and when something does enter the sludge, multiple worms will attack it until it is dead. They even eat the dropped items, whether it be one sticky resin or a stack of Iridium Plates.
I hope that these ideas will help in the development of this modification. Thank you for taking your time to read this and develop such an awesome modification.
and it is true, they do that in star trek 
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