With respect to spice, I feel that it simply isn't important enough in game. I think there should be something like a global spice counter (spice resources per turn per civ) which, say, gives each civ a flat solaris bonus once it reaches a certain milestone. For example, 1000 solaris (adjusted upward for each era) per civ each time the global counter hits 1000 spice. It would be nice to increase the importance of solaris as (I think it was) keldath mentioned in a different post...
This global dynamic would help to level the playing field. But to encourage extra spice production, each civ could have their own spice counter. Once they reach a certain quota, they could receive special, otherwise unobtainable units from, perhaps, their home world (which could tie in to your idea about the homeworld screen). Or perhaps from the Spacing Guild who could receive something every time a civ uses this feature, but is otherwise unable to do it themselves.
Finally, I really think the spice harvester unit should return. It should have sufficient movement points to enter an adjacent spice plot and immediately begin production of a spice harvester improvement. Additionally, I would personally like to see a very expensive harvester unit that could make an improvement in one turn, and perhaps has additional defensive bonuses. Maybe make it a national unit...
As for other suggestions: I have found that most civs NEVER switch to terraforming, except the Fremen ones. Perhaps this is because I have the terraforming victory turned off (then again, I hate all victory conditions and never actually play to achieve one...) This is unfortunate because I think the terraforming mechanic is impressive and is significantly better than the spice civic, which could use some improvements itself. Perhaps if you choose to implement something like my spice quota mechanic, there could be significant bonuses to that. Alternatively, the spice civic could offer something like access to a special spice oriented corporation. It would have to be something that would provide an ultimate benefit to every city it is in (instead of relying on the corporate HQ to counteract the weird maintenance mechanic).
I think you guys should also consider altering what terrain cottages can be placed on. While their importance is greatly reduced in this mod (thankfully!) due to the increased importance of trade routes, civs that start on primarily rocky continents almost always do absolutely terribly. Ahriman already mentioned this, I just wanted to second it.
Finally, and I think this is primarily just a personal preference, but I would like to see how the AI chooses city sites changed. Way too often they build cities way too close together, simply to get access to, say, a meagre water and one other special improvement. These cities simply detract from precious city plots of the main ones. City plots are significantly more important in this mod due to the (justified) harshness of deep desert absent the presence of spice. This mod would be much better served with fewer cities, in my opinion. Actually, a fairly radical approach would be to use the 3-plot radius mechanic used in FFH, with the AI modifications that knows how to use it. Like I said, just a personal preference.