Regarding the UI...not exactly a suggestion, more of a question. I love the node based layout and navigation...however I am curious how you will show other information that is inevitably going to be found AT nodes. For example, if I am navigating a trading outpost, and I find a store selling ships. I navigate through the nodes for each ship...how do I SEE the ship? Will three be a more cohesive UI presentation for a ship, as well as it's key data points? While it is interesting to know that below the ship node, all the relevant data nodes describing it will probably also exist...but to be honest, that isn't the most useful means of displaying the information about a ship that I might want to buy.
Instead, I think it would be nice to have call-outs or something similar, where instead of having to navigate the graph to learn about the ship, I can simply call out a data card of some kind that nicely displays the information about it in a more human-readable form. Show a wireframe of the ship design, along with its key data points or stats like mount points, tonnage, speed capabilities, weapon capabilities, etc. etc. in one largely text-based UI that I can rapidly read through.
Extending this further, if I want to compare ships, I should be able to pull up callouts for multiple ships from said vender, and array them on the screen in such a way as it is easy to compare data points/stats. Similarly, it would be useful to have the ability to pull up a callout that collapses a graph hierarchy for just about anything in the world...if ships have scanners, and I'm able to scan other ships, stations, asteroids, worlds, etc. for useful data points, while I think having a fully detailed graph menu is useful to completely explore every aspect of said objects, it would still be nice to pull up a callout linked to those objects that more cohesively displays the key data points and statistics in a more human readable form. The ability to switch or jump between graph view and callout view (and even link the two together on the same screen) would be immensely useful.
Sorry if this disrupts your current universal UI concept...but I think there is an "immediate-mode usability" issue if the graph was the single sole UI concept in the game. In other words, when you need quick access to important information about something, digging about in a graph can become tedious, even if each distinct kind of thing in the universe has a differently shaped graph, it doesn't display related information from sibling nodes or child nodes (or even ancester nodes) in a way that allows you to rapidly absorb the information then move on with gameplay. I don't want you to get rid of the graph UI...I think it is exquisite. But extending it a bit to provide high-importance data and statistics in less hierarchical and more flat callouts or popups or whathaveyou is probably going to be important in the long run, from a usability standpoint.
(BTW, I speak from some experience. I'm a software engineer myself, and I've done work with mass data mining with Hadoop, immense graph databases with trillions of connections and billions of nodes, etc. While graphs are most certainly a useful way of organizing related and hierarchical data, there is no question they have their drawbacks, and presenting critical information to a user always results in querying the graph for the relevant data points, then reorganizing it into neat, simple little UIs for the "lesser people" (read as: the average non-code-wiz, non-math-wiz human being. ;-P). Usually, development of those simple UIs involves countless man hours of custom web UI development. With your knowledge of procedural information generation, I have no question you could probably whip up some kind of procedural callout-card UI generator to solve the problem for any critical node in your entire game engine graph.)