spirit of Transcendence
It looks like your massive outpouring of text is basically agreeing with what I said earlier. Defining a player character in a game like this is annoying, because players usually make up their own characters as they go along, whether they be "space pirate," "military cadet," "intergalactic pimp," or whatever. However, it would be nice to have a few more variable story elements that would allow a character to choose sides/make moral choices/etc... to help portray the character that they're envisioning a little more firmly in the game world. There may be a set end result (destroying the iocrym command ship and going to the galactic core) but there should be many ways to get there, kind of like in the fallout series.