lol. well there IS limits to what you can do. yes you can have multiple kinds of starbasses depending on what you design them as. you cant really add/remove the current 3 currencies (crystal, metal, credits). your limited to grav wells as far as movement goes, although you can make the grav wells huge. you can have essentialy as many planets as your comp can handle, same goes for ships if you mod that in. you can mod planets but thats verry limited. you can redo the stats of all ships however you like. you can retexture ships, re rig ships (change where effects originate/fire from on a model/mesh). you can create custom descriptions for all ships as well as add in new ships. you can remodel any building you want if you got a 3d program with the proper extenchions. diplomicy is pretty much linear in the game, you can modify what missions they give, what tolerences you can do stuf, but when it comes down to it, no buildings affect this. as far as science is conserned, planet moduals (buildings) are essently the only way to research new items. as far as space colonies go, thats up to the person, you can create starbases that you build that can hold people on them, or you can create planet mesh/texture to look like a staarbase.
now for the fire few questions.
Modeling programs: (these all have HUGE leraning curves and take hundreds of hours to get good at)
SoftImage XSI - free version, verry limited. if you buy it, its a lot better
3DS Max - trial version, 30 days. my prefered program.
Maya - not sure about any trials or whatnot since i dont use it, not sure if you can convert the models from the program into sins, only 2 that i know of is the 3ds masx plugin for .mesh conversions as well as the XSI tool to change .xsi into .mesh.
Texturing programs:
Photoshop - 30 day trial. generaly the prefered texturing/editing program out there, probly one of the most well known as well. has a learning curve to it but what does not now days. easiest program to sue for .dds conversion (required for textures)
Gimp - a free version of photoshop, has a lot of simularities, not as powerfull but hey, its free, who can complain. may have problems converting textures to .dds though.
PaintShop Pro - not sure about this one, ive never used it before, hear it does have limitations though. dont think this one can do .dds format files but i could be wrong.