Something little... but you know how trade grows by 1% per turn up to 20%, where the 20% is moddable (like in P&N it's 10%)? Well, how about if the rate was moddable too, and could be set for each of the individual resources and points - so you could have Minerals, Organics, and Radioactives trade growing by 1%/turn up to 10%, say, and Research and Intel trade growing by half a percent a turn up to 5%.
Also, MOO1/2 had this and I think it adds a bit of realism - establishing trade or research treaties doesn't initially produce a profit - in fact it initially costs money to set up trade routes, but after a few turns you start making money.
(I wish I could be on the design team for the next SE game... too bad Aaron does most of this himself!
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