-It would be nice if religion (Belief, aforementioned) was as important as it is in FFH, or if cities could "convert" to another faction as a result of: Culture, Belief, Probe Team influence, etc. I think this would also beg the use of "inquisitor" style units.
-It would be nice if civics functioned as they did in SMAC, with strong correlation to wonders. Thankfully, a lot of the Social Engineering mechanics carried over to Civics, so I personally think this area needs the least work to be effective.
-It would be nice if Ecology worked the way it did in SMAC, with Lifeforms appearing in fungus and prioritizing high-industry bases for pillage and attack...and further, if they can be captured by appropriate factions (or civic-users). I think these are both very possible, given what other mods have done with similar concepts (Enslavement). Also, at various trigger-points, there should be planet-wide health drops and worm signs...er...spawns. FFH does a fab job of that sort of thing; I think someone already mentioned use of the Armageddon Counter from FFH.
-I really would rather not see a "Unit Builder" Screen, or Modular Units. Civ 4 is just not made for it, nor is the AI. "Purchasable" promotions with improving weapons/armor, I can see (the "crew" mechanic from FFH comes to mind). One possible approach is to leave weapons and armor in the purchasable promotions realm, and make "Default" platforms for each Unit Chassis, one per reactor level, with improving "default" weapon/armor promotions based on other available techs.
-It would be nice if probe teams had more functions than spies do in current civ. Seems low priority, but other mods have made interesting accomplishments.
-Without too much hassle, I could see for improvements: Cottages = Forests (they take time to grow before the "tree farm buildings" aid them, to make them slightly less powerful than in SMAC; Forest spread would only create "new growth" that had to be worked to improve), Watermills = Gone, Farms could provide increasing benefits based on humidity of terrain (accomplished by making seperate farm improvements for each terrain), Mines could do the same, and Solar Collectors could also do the same, albeit for features (Hills or Not Hills). Fungus is, of course, jungle, and it is about as nasty at game start as jungle is in Civ 4. As for the others: Boreholes, Mirrors, Humidifiers; I think they should only be in if they can be actively targetted by native life, and function as they did in SMAC.
-I'm glad that UN mechanics are high priority, that was easily one of the best ideas in SMAC, albeit sometimes silly due to AI. Civ 4 UN is...it shouldn't have made it into the final game, and I'm surprised it wasn't improved in Warlords.
-Unity Pods, Sea Unity Pods, and Landmarks: Since you will absolutely need a custom mapscript for this anyhow, preferably one with artifical windspeed/moisture/altitude as dominant factors, it would be nice if it made landmarks, too. Unity Pods, and the many things they did, were fundamental in creating that "exploring an unknown world" feel, and they should be around in abundance with most or all of their original effects.
-Sea Bases: I wish. I don't see the AI liking it.
-Offworld/Satellites: Satellites Advisor Screen. Seems necessary, and doable.
-Convoys: No. Unbalancing, unnecessary implementation. I hope this isn't in.
-Blind Research: I think it should be in, there are already FLAVOR values for the AI, and it doesn't sound hard compared to what other mods have accomplished (tech leaking, for example). It would also remove a burden of choice from the AI, such that what the AI researches changes from game to game, instead of always avoiding X, Y, and Z technologies (Any Popped Religious/Free Tech/Free GP Tech, etc. from Civ 4)
-Specialists: SMAC had a colorful array of them; I think the GP mechanic will sync well with it. More or less:
-Librarian- Great Scientist = Master Librarian, no change
-Technician- Great Merchant = Master Technician, "trade mission" replaced by "Collector Optimization" for a friendly city, improves solar collector functionality in its radius.
-Psychologist- Great Prophet/Great Artist = Master Psychologist, Holy Shrine replaced by "Propaganda" ability, converts city to Faction belief par missionary and adds Factional culture; when added to city, increases happiness.
-Engineer- Great Engineer = Master Engineer, no change (creative!)
-Doctor- New = Master Surgeon, can instantly build any two biomedical-themed buildings (Creche, Hospitals, Recycling Tanks, etc.), when added to city, increases health.
-Transcend - New = Omega Transcend, does something so amazing it can't be mentioned.