I just stumbled across this thread, and I have some ideas regarding "traits" and civics.
I don't know if it even makes sense posting about this now because there have already been some decisions about the topic, but I'll do it anyway.
First about "traits": I think the CIV traits should all be ditched and every faction get some unique advantages and disadvantages to make them much more distinct than the more than 30 civs, and make them so that some profit much more from certain civics than others.
The civics: I guess the rebirth of the original modular SMAC system might be too much programming work, but the civics could be designed to grant synergies like for example Representation+Mercantilism.
It should always be able to buy production, and every faction should be able to run every civic.
I'll give two exapmles for The Hive and Morgan Industries and some civics.
The Hive
+1
per 2 units in the city
every city stores 20% food
-25% cost for rushing production
-1 trade route
-15% culture
Morgan Industries
+1
on every tile with at least 2
+ 1 base
from trade routes
units require +20% experience to gain new promotions
+15%
in every city
Now some Civics
Police State
+ 1
per unit in the city
+ 1 free unit per 4 poppulation
-10% culture
You see that The Hive will benefit more from this civic than other factions because it a) increases their police bonus to + 3 per 2 units, helping to keep the fast growing population "happy" and b) makes it affordable to have larger garrisons. On the other hand the culture penalty gets even worse.
Planned Economy
-25% rushnig cost
+ 2
per city
- 50% trade yield
The Hive already pays only 75% to rush production, so with this civic the cost for buying things will effectively be cut by 1/3. While Morgan Industries can still use this as a production civic the trade penalty will hurt them more than any other faction, The Hive on the other hand won't be affected much by the loss because their trade income isn't very high anyway.
Free Market
+1 trade route
+ 50% trade yield
-2
in all cities
A good civic for people who have many open borders except for The Hive and especially useful for Morgan Industries although health might become a serious issue.