One thing that's always bothered me about that other space game is lack of things to do later in a career save. Once you've unlocked the full tech tree the science aspect of it all becomes almost irrelevant, and once you've seen one medium-sized, vacuum body you've seen them all. I don't know if there is or will be a career or science-gathering aspect to SR2 (waiting for the GOG release) but if there is, it would be cool if it was more than just "use this part this many times in every biome".
A small mini-game or something, that gets progressively harder the more science you gather, or unique (perhaps randomized) aspects to certain bodies that "force" you to visit them to progress would be really nice for the long-term.
Robust modding support could cover this I suppose, but it would be nice to at least have the architecture for things like this in the stock game.
look out for alien easter egg