I don't think we had any idea that the Gekkostate were eco-terrorists or anything other than anti-government when Renton hopped on, and their mission wasn't fully revealed until episode 29 or so.
Lots of people complained about jargon early on in Eureka seveN (what about a Seven Swell), and there was the same deal with the lack of cooperation between the local and state governments in the early episodes. Though Dewey's metaphorical musings didn't begin until episode 4, it wasn't long after (6 or so) that the word coralian first popped up, and even then just what a coralian was wasn't explained for nearly half of the series.
There is a lot that can be inferred, but it would be very difficult for most people to do so without seeing the full context of the series. Sure, upon rewatch, Eureka seveN makes sense from the very beginning, but it can often be confusing for a first-time watcher.