Something else interesting here is that we were shown a prototype in the Kickstarter video of the 'low-level' generation, flying in and amongst the clouds, and the video from 2014 mentioned by @Tinman is of the 'high-level' generation showing the large scale of a gas giant. They have been tackling this problem from both ends for some time; bringing them together is crucial - but I wouldn't be surprised if they had already done this. There are, however, other challenges that have yet to be overcome (or at least shown to us, though I'm hoping this will be the big thing for season 3):
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1) The generation needs to produce clouds of different types (gas giant cloud layers should be different from those on an Earth-like World or rocky moons with a thin atmosphere, although there would be some elements in common) and also have the concept of different layers within an atmosphere where different types of clouds form based on the conditions.
2) The flight model needs to be able to address the different handling of ships in an atmosphere in potentially extremely windy conditions. The wind speeds in the atmospheres of gas giants in our own solar system are of the same order as a typical ship's maximum cruise speed, greater in some cases. It would certainly be amazing to have 'Cloud City' type outposts inside the atmospheres of gas giants but could I land an Anaconda rigged for mining in a 200m/s crosswind? Perhaps these outposts would only be built in the eyes of long-lasting storms where the wind speeds are low, although there might be some hidden (possibly damaged or well-shielded) elsewhere, possibly needing assistance, possibly with unusual missions.... (OK, getting myself excited, sry!)
3) Precipitation. Good luck with this - procedurally generating a system that rains/hails/snows the appropriate material in the right places is going to be tough - I would not be surprised if we get atmospheric flight but where worlds with precipitation are off-limits until a later season. From the descriptions of some worlds I have seen, there could be iron rain on the surface - wouldn't want to be out in that in my SRV! With precipitation, there is also the prospect of fluid flow over the surface - your SRV could be washed away in a flash flood! There is a lot to handle for this, so I'm not expecting to see it any time soon - though perhaps some weather effects like lightning discharges may be easier to manage.
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Is volcanism really confirmed as definitely coming this season? I thought it was on the 'maybe if there's time' list. If it is that would be great! The Voyager image of a volcanic plume seen over the limb of Io is one of the classic images of our exploration of the solar system, along with the eruptions on Enceladus seen by Cassini. Even if no particular gameplay is attached, there is plenty of potential for spectacular images and videos of this happening in-game.
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