@ GeoModder -- I'm only just delving into Python now, so I haven't yet touched aspects like terraforming, though I am secure in the knowledge that others have done so successfully. It may end up being possible to have 2 improvements per tile by using a buildable feature (e.g. forest) as improvement 1 and improvement (e.g. lumbermill) as improvement 2, but I'm not sure I want to follow SMAC that faithfully, as I'm not sure what being able to do so adds to gameplay. (Other than the fact that my analogue to fungus is a feature, and so far only improvements, not features, benefit from technology and civic choices as the game progresses).
I'm playing around with a potentially interesting (or disasterous) replacement for religions right now that, I hope, captures some of the flavor of SMAC but in other ways totally re-writes the rules.
Game balance has been a major issue. I've only done work on the "ancient" era, and so far it's a bit dull -- perhaps because I've not implemented most bonuses yet. My imagination runs only so deep, so I'll be glad to release this into the wild, so to speak.
As for my own answers to the questions I posed:
I love the storyline, the atmosphere of the game, and at least the first few times I played, the feeling of discovery that the interludes and scripted events provided. I love Planet as a character; I love learning to talk with her. (You can tell I played Diedre heavily). I love the depth of the backstory and "forward story" that's revealed in parts as you read and listen to the quotes associated with the techs and facilities. (For example, the "official" story seems to involve some kind of Gaian-Spartan conflict that the Gaians win).
I liked civics and thought the concept of having civics that, in turn, pulled levers on the "master character" of your faction was a neat mechanic. Civ4 went halfway there and trades off between flexibility and specificity (you can do things with the civics system in Civ4 you can't do in SMAC, but if you try running off the road things can get hard, fast).
I thought probe teams had more potential than was used, and am glad to see spies back in Civ4, albeit without any new features. I would like to explore the idea of multi-arena warfare and how to have a fun game running a "cold" war.
I wasn't so hot on the workshop myself, as I found it tedious, though the first few times it was certainly fun to create colonizing needlejets.

I think one problem was that there were too many weapons upgrades -- something that Civ4 handles well, up until the turns roll by too quickly at the end.
I also didn't like how the game seemed to bog down starting in the mid-game. I think that may have more to do with the need to micro-manage units than anything else, though Civ4 improves on the tech tree concept over both SMAC and Civ3, IMHO. I think Civ4 also has the better concepts around building specialized cities rather than spamming.
Finally, as someone invested in the game storyline I think there needed to be more explanation for why a faction could figure out how to map the genetic sequence but not know how to build boats or planes -- or, eventually, to contact Earth.